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Bygul

Simulate tiled-amplicon sequencing reads from two sample genomes mixed at chosen proportions, given a reference and a primer BED scheme.

License: BSD-2-Clause. Source code.

What it simulates

Bygul simulates tiled-amplicon sequencing, the method used for SARS-CoV-2 genome surveillance. It takes two or more sample genomes, a reference and a primer BED file. It finds each primer pair in each genome, cuts the amplicon between them, and simulates paired-end reads with wgsim (or mason or ART). It mixes samples at proportions you set. It returns one pair of FASTQ files with all reads, plus per-sample amplicons, reads and a stats table.

Key assumptions: an amplicon exists only if both primers match the genome within --maxmismatch mismatches. Every amplicon gets the same read budget (--readcnt).

When to use it

  • Test a lineage-deconvolution or mixed-infection tool on known mixtures.
  • Study amplicon dropout: which primers fail on a variant genome.
  • Check a primer scheme against a new variant.

Alternatives on biosimhub: wgsim and DWGSIM simulate whole-genome short reads without primers. InSilicoSeq simulates Illumina metagenomes.

Install it yourself

Bygul 4.0.5 is on bioconda (dry-run resolved, build pyhdfd78af_0, 25 kB).

conda create -n bygul -c conda-forge -c bioconda bygul=4.0.5
conda activate bygul

Minimal command:

bygul simulate-proportions --genomes s1.fa,s2.fa --reference ref.fa --primers primers.bed --proportions 0.8,0.2 --outdir results

Defaults from --help: 500 reads per amplicon, read length 150, insert size 200 (SD 10), one mismatch allowed, wgsim error rate 0.0001, 4 threads, simulator wgsim. The BED name column must look like scheme_3_LEFT.

Run the tested example

This recipe builds Bygul in a container and runs the example below. It needs Docker and nothing else. It last ran on 2026-10-12 in 1.1 s.

  1. Download bygul-recipe.tar.gz (Dockerfile, example sample1.fa, sample2.fa, reference.fa, primers.bed, run.sh).
  2. Unpack it and run the script: 
    tar -xzf bygul-recipe.tar.gz
cd bygul
sh run.sh
What run.sh does 
docker build -t biosimhub/bygul:4.0.5 .
mkdir -p out && chmod a+w out
docker run --rm \
  --user "$(id -u):$(id -g)" -e HOME=/tmp \
  -v "$PWD/in:/work/in:ro" -v "$PWD/out:/work/out" -w /work/out \
  biosimhub/bygul:4.0.5 bygul simulate-proportions --genomes /work/in/sample1.fa,/work/in/sample2.fa \
    --reference /work/in/reference.fa --primers /work/in/primers.bed \
    --proportions 0.7,0.3 --threads 1 --readcnt 100 \
    --maxmismatch 1 --insert_size 200 --insert_size_sd 10 \
    --read_length 150 --wgsim_error_rate 0.0001 \
    --outdir . > out/bygul_log.txt

Inputs are read from in/ and results land in out/. Change the values after each option to run your own case; the parameter table lists them.

Expected output

FileSize
bygul_log.txt335 B
reads_1.fastq260.3 KB
reads_2.fastq260.3 KB
sample1/amplicons/amplicon_1.fasta383 B
sample1/amplicons/amplicon_2.fasta413 B
sample1/amplicons/amplicon_3.fasta413 B
sample1/amplicons/amplicon_4.fasta413 B
sample1/amplicons/amplicon_5.fasta413 B
sample1/amplicons/amplicon_6.fasta413 B
sample1/amplicons/amplicon_7.fasta413 B
sample1/amplicons/amplicon_8.fasta413 B
sample1/amplicons/amplicon_stats.csv1.2 KB
sample1/reads/amplicon_1_contig1_1.fastq21.8 KB
sample1/reads/amplicon_1_contig1_2.fastq21.8 KB
sample1/reads/amplicon_2_contig1_1.fastq21.8 KB
sample1/reads/amplicon_2_contig1_2.fastq21.8 KB
sample1/reads/amplicon_3_contig1_1.fastq21.8 KB
sample1/reads/amplicon_3_contig1_2.fastq21.8 KB
sample1/reads/amplicon_4_contig1_1.fastq21.8 KB
sample1/reads/amplicon_4_contig1_2.fastq21.8 KB
sample1/reads/amplicon_5_contig1_1.fastq21.8 KB
sample1/reads/amplicon_5_contig1_2.fastq21.8 KB
sample1/reads/amplicon_6_contig1_1.fastq21.8 KB
sample1/reads/amplicon_6_contig1_2.fastq21.8 KB
sample1/reads/amplicon_7_contig1_1.fastq21.8 KB
sample1/reads/amplicon_7_contig1_2.fastq21.8 KB
sample1/reads/amplicon_8_contig1_1.fastq21.8 KB
sample1/reads/amplicon_8_contig1_2.fastq21.8 KB
sample1/reads/merged_reads_1.fastq174.4 KB
sample1/reads/merged_reads_2.fastq174.4 KB
sample2/amplicons/amplicon_1.fasta383 B
sample2/amplicons/amplicon_2.fasta413 B
sample2/amplicons/amplicon_3.fasta413 B
sample2/amplicons/amplicon_4.fasta413 B
sample2/amplicons/amplicon_5.fasta413 B
sample2/amplicons/amplicon_6.fasta413 B
sample2/amplicons/amplicon_7.fasta413 B
sample2/amplicons/amplicon_8.fasta413 B
sample2/amplicons/amplicon_stats.csv1.2 KB
sample2/reads/amplicon_1_contig1_1.fastq10.7 KB
sample2/reads/amplicon_1_contig1_2.fastq10.7 KB
sample2/reads/amplicon_2_contig1_1.fastq10.7 KB
sample2/reads/amplicon_2_contig1_2.fastq10.7 KB
sample2/reads/amplicon_3_contig1_1.fastq10.7 KB
sample2/reads/amplicon_3_contig1_2.fastq10.7 KB
sample2/reads/amplicon_4_contig1_1.fastq10.7 KB
sample2/reads/amplicon_4_contig1_2.fastq10.7 KB
sample2/reads/amplicon_5_contig1_1.fastq10.7 KB
sample2/reads/amplicon_5_contig1_2.fastq10.7 KB
sample2/reads/amplicon_6_contig1_1.fastq10.7 KB
sample2/reads/amplicon_6_contig1_2.fastq10.7 KB
sample2/reads/amplicon_7_contig1_1.fastq10.7 KB
sample2/reads/amplicon_7_contig1_2.fastq10.7 KB
sample2/reads/amplicon_8_contig1_1.fastq10.7 KB
sample2/reads/amplicon_8_contig1_2.fastq10.7 KB
sample2/reads/merged_reads_1.fastq85.9 KB
sample2/reads/merged_reads_2.fastq85.9 KB
First lines of bygul_log.txt 
Reading and preprocessing the primer file...
Spinning up parallel execution for 2 samples...

Genome: sample1
  Total ambiguous bases: 0
  Contig lengths:
    sample1: 3000

Genome: sample2
  Total ambiguous bases: 0
  Contig lengths:
    sample2: 3000
First lines of reads_1.fastq 
@2_0_195_395_0:0:0_0:0:0_0/1
TAACGTTAGCCTTTGCTCACTGTCCGTCAGTAAAACTCTAGTTAGTAACGCTAGTTAAGGGCAATGCCGCCGCGGAACAGTTGTAGTTAAGTAGAAGACCTAAAGGCTGGTCCGCGAGTCACGTTTTTTCCACGGCTCGATCATTGATGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_189_381_0:0:0_0:0:0_1/1
GCTCACTGTCCGTCAGTAAAACTCTAGTTAGTAACGCTAGTTAAGGGCAATGCCGCCGCGGAACAGTTGTAGTTAAGTAGAAGACCTAAAGGCTGGTCCGCGAGTCACGTTTTTTCCACGGCTCGATCATTGATGCTACATTCCGTGATC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_9_189_0:0:0_0:0:0_2/1
AACTTAATGTATAGTTCTTGAATATCATGGGGATCCAGCCATGTGTGGACCTGAATTCCCTATGCGCTCGAACTGGGTAACACAATCAATGGGTTTTAGGTCACCGAACCCGCAGGATTGCGTATTCAAAGATTTTCTGGAACGGCCGTC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of reads_2.fastq 
@2_0_195_395_0:0:0_0:0:0_0/2
TCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGAATGTAGCATCAATGATCGAGCCGTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCTTCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCTTAACTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_189_381_0:0:0_0:0:0_1/2
TGAACCTCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGAATGTAGCATCAATGATCGAGCCGTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCTTCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_9_189_0:0:0_0:0:0_2/2
TCCCTCACAATAGAATCATAGTTGGACGCGCGACGGCCGTTCCAGAAAATCTTTGAATACGCAATCCTGCGGGTTCGGTGACCTAAAACCCATTGATTGTGTTACCCAGTTCGAGCGCATAGGGAATTCAGGTCCACACATGGCTGGATC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/amplicons/amplicon_1.fasta 
>1_0
CCCGGCCCCTGAGTCCGAGGAGAGGGTGCTTCAGAGTATGTATACCACTGGGTAGGATAC
GGCGGAGGGCACGTCAATACGGTTCAAAGCCCTACTGCATGCTCTTGTGGTTCATCTGCA
TGGAGAGGGTGGGCATGGGTGGGGGTGCTGGCCCGTGATCTGGACCTCCCATCCACAGCT
CATTGTACCGAGTGTAGAGAGGGGCTTGTCCTTCCAGATAGCGTTTCTGTTTCGGTGTAG
GTGCTAATCGACTATGCTACTGCGGTTAACGGGGATGGCAAGTACATTTTTTCGTAGATG
TGCCTTGCTAACGAAAGTATTAAACACGTCCCTCACAATAGAATCATAGTTGGACGCGCG
ACGGCCGTTCC
First lines of sample1/amplicons/amplicon_2.fasta 
>2_0
TAAACACGTCCCTCACAATAGAATCATAGTTGGACGCGCGACGGCCGTTCCAGAAAATCT
TTGAATACGCAATCCTGCGGGTTCGGTGACCTAAAACCCATTGATTGTGTTACCCAGTTC
GAGCGCATAGGGAATTCAGGTCCACACATGGCTGGATCCCCATGATATTCAAGAACTATA
CATTAAGTTGAACCTCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGA
ATGTAGCATCAATGATCGAGCCGTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCT
TCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCTTAACTAGCGTTACTAACTAGAG
TTTTACTGACGGACAGTGAGCAAAGGCTAACGTTATTCCGT
First lines of sample1/amplicons/amplicon_3.fasta 
>3_0
CTAACTAGAGTTTTACTGACGGACAGTGAGCAAAGGCTAACGTTATTCCGTGAGCACGGG
ACATCCATTCTTCGTGAGCTACAGCTCGAGGATCAGCTTCTAACCACGCGATGCAGAACC
GGCTACTTTAAGCATTGATGAATGCGTCGTAAGTGATACTCGACGATTCTCATGCAACGA
AGTTAACCTATAGTAACTTACATTTTACGCGCTAGCTTCGCTGGAACTAATATCCATGTC
TCAGAACTAGCGGCCGAGAATGGGTTCCGAATCCTAAACTCCGACATGAGTTAAGGTTGC
ATACTAGGTCTGATACTAAAAGCGGGGTCAGGAGTCCGTCCAGAATATAATATTCAAAAA
TGAGAAGGTGGAGTTTCCGGCTACGATTTCCCTCTGACTGT
First lines of sample1/amplicons/amplicon_4.fasta 
>4_0
TATTCAAAAATGAGAAGGTGGAGTTTCCGGCTACGATTTCCCTCTGACTGTCCCTGGGAC
GTGGTAAAGAAGCATCGGATGAGAGGTTAAGACAATATTACTAGAGGATTACCAAATTAG
GTTACCTCCGACGATGTGGCGTTTACCTATCCCCATGTCTAGGGAACAGTTGGAGCTGTG
CGCAATCGTGTTGGACTATTGACATACCCCTATTCGACCAGTGCAGTAGACTATACCACT
TTTGAATCATCAGCAGACCTAATAGCTTCATCCCTTCTAGTCGACTTTCCGGACCGATGC
GCACTAATGATCGAAGTGTGTCTTTACTGAATCAGAAGTCGGAGAAAATTCTGCTGTACG
AGATGTACGTAGCGATGATGATACGGGTGATTCTTACATGA
First lines of sample1/amplicons/amplicon_5.fasta 
>5_0
CTGCTGTACGAGATGTACGTAGCGATGATGATACGGGTGATTCTTACATGAGGTACATCG
AAAAAGGGTCATTGCGTTTACGTGAATGGGATTTGCCTGGCCTATGGCCTTAGTACCTCT
AAGAGGGCAACTAGTCACGGCGTAAACAGACAAGGGTCGGATCCTAGTCACTAGTAGATC
AACGGCTAAGTGGGCGTCACCAGACCCTCGCCCATCTGGACTAGTAGACCGTGTGCCTCA
ATCGACGCGTGAGGACACGTTGATTTCTTATACGGCGTCTCAGCTTTCTTTTCCGCCAAT
TACATCAAATTCAAGTGCCTTGAGATACCGGGCCTATTCGTGCGTAGACCGGCGCGATGA
GACAATGCCGGCATTTAAGTAAAGGTCCGGGATTATTGTAG
First lines of sample1/amplicons/amplicon_6.fasta 
>6_0
GGCGCGATGAGACAATGCCGGCATTTAAGTAAAGGTCCGGGATTATTGTAGACTAACTCT
GCCAAATTATGCGTGCCTTGAGAGTATACACTCCGCATCCTTCTCGTATGATGGCAGGGA
GGGCCTTGGTTCCAGAACTTATCGCTAATGCGCTGGGTGCCATGCATGGAGCGTCTCTTG
ACATCAGGAAGTACCGGCTCCTGTTGGGGAGTTCGAAAATAGCTTATGGGACATCAGGCC
ATACTACTAGAACCTTGACCTGTACTGCATATCGTTTTCGGTTAAACTCGGTAGGTAAAA
ACACTTGTCGCCAGGATTCGCCACTCAAGGTTTATAGCAAAGAATACTACTGAAACTGGC
GTCCCCCATTAGTCACATCCTGCGAGGCGGCTCTCGACGGC
First lines of sample1/amplicons/amplicon_7.fasta 
>7_0
TGAAACTGGCGTCCCCCATTAGTCACATCCTGCGAGGCGGCTCTCGACGGCATAACGGGA
TCTCTCCGGCTAAGGTCGAATGAGTTTAGTCTGAAGGTGGCAGCGCACACGACGGTATGT
TTCACCGCCGTCTGTTCGGAGCTATAGCATCATTAGGCCTAGCTATGGCGCCCCCGTTTC
CTACCGCAGCTACTGCATGCACTCGTTACGACAAAGTTCCTTTATTGGCTACAGGATTCT
ATCGTTCCGGCCTAGTGCGGGGGCATCTGCAGGCCGTCGTCCGTCCTACGTAAGGCTCAT
GCGTACGGTAACAATAGTTGGTTAGACCTGACCACGCGTGATCCGCGCCTCCTTCCCCGC
GTCACGTTAGGTGAAACCCTGCCCCGCTTAGCACGTCTCAT
First lines of sample1/amplicons/amplicon_8.fasta 
>8_0
CCTTCCCCGCGTCACGTTAGGTGAAACCCTGCCCCGCTTAGCACGTCTCATGCTAACCCT
CTTTCCTGAGGGTAAAGGAACGTGCAATCCCGAAAAAGGTGAATGAAAGGCTGGGACGCT
CCTGGTTTGGGGCGCTCTAGGTGTTGTGGCTTGAACGTTAGCACCTCGGCTTCCGAATTG
ATACTAGGCATCCTATCGAACACTATTAGCCGCCCTTCTTCATATTACTGTGGGTACAGA
CAAATAGAGGAGGTGTACGGTGACTAGCGGGTATCTATCATTAGGAAAGGGTACCGGCAT
CAGGAAGAAAGCACCGTCCAATGATCACCACGGCTCCTTGCTTGCCACCGAAGCCATAGA
CATATGAATAGCCCGCTGTGGCTCTCCGACGAAGTGCGCGG
First lines of sample1/amplicons/amplicon_stats.csv 
amplicon_number,primer_seq_x,primer_seq_y,ambiguous_bases,primer_start,primer_end,left_match,right_match,amplicon_length,contig_id
1,CCGGCCCCTGAGTCCGAGGAGAGGG,TAGTTGGACGCGCGACGGCCGTTCC,False,30,375,CCGGCCCCTGAGTCCGAGGAGAGGG,TAGTTGGACGCGCGACGGCCGTTCC,370,sample1
2,AAACACGTCCCTCACAATAGAATCA,TGAGCAAAGGCTAACGTTATTCCGT,False,350,725,AAACACGTCCCTCACAATAGAATCA,TGAGCAAAGGCTAACGTTATTCCGT,400,sample1
3,TAACTAGAGTTTTACTGACGGAAAG,CCGGCTACGATTTCCCTCTGACTGT,False,700,1075,TAACTAGAGTTTTACTGACGGA(C)AG,CCGGCTACGATTTCCCTCTGACTGT,400,sample1
4,ATTCAAAAATGAGATGGTGGAGTTT,GATGATACGGGTGATTCTTACATGA,False,1050,1425,ATTCAAAAATGAGA(A)GGTGGAGTTT,GATGATACGGGTGATTCTTACATGA,400,sample1
5,TGCTGTACGAGATGTACGTAGCGAT,AAGTAAAGGTCCGGGATTATTGTAG,False,1400,1775,TGCTGTACGAGATGTACGTAGCGAT,AAGTAAAGGTCCGGGATTATTGTAG,400,sample1
6,GCGCGATGAGACAATGCCGGCATTT,ATCCTGCGAGGCGGCTCTCGACGGC,False,1750,2125,GCGCGATGAGACAATGCCGGCATTT,ATCCTGCGAGGCGGCTCTCGACGGC,400,sample1
7,GAAACTGGCGTCCCCCATTAGTCAC,CCCTGCCCCGCTTAGCACGTCTCAT,False,2100,2475,GAAACTGGCGTCCCCCATTAGTCAC,CCCTGCCCCGCTTAGCACGTCTCAT,400,sample1
8,CTTCCCCGCGTCACGTTAGGTGAAA,TGTGGCTCTCCGACGAAGTGCGCGG,False,2450,2825,CTTCCCCGCGTCACGTTAGGTGAAA,TGTGGCTCTCCGACGAAGTGCGCGG,400,sample1
First lines of sample1/reads/amplicon_1_contig1_1.fastq 
@1_0_131_344_0:0:0_0:0:0_0/1
GGGCATGGGTGGGGGTGCTGGCCCGTGATCTGGACCTCCCATCCACAGCTCATTGTACCGAGTGTAGAGAGGGGCTTGTCCTTCCAGATAGCGTTTCTGTTTCGGTGTAGGTGCTAATCGACTATGCTACTGCGGTTAACGGGGATGGCA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@1_0_158_363_0:0:0_0:0:0_1/1
ATCTGGACCTCCCATCCACAGCTCATTGTACCGAGTGTAGAGAGGGGCTTGTCCTTCCAGATAGCGTTTCTGTTTCGGTGTAGGTGCTAATCGACTATGCTACTGCGGTTAACGGGGATGGCAAGTACATTTTTTCGTAGATGTGCCTTG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@1_0_117_314_0:0:0_0:0:0_2/1
TGCATGGAGAGGGTGGGCATGGGTGGGGGTGCTGGCCCGTGATCTGGACCTCCCATCCACAGCTCATTGTACCGAGTGTAGAGAGGGGCTTGTCCTTCCAGATAGCGTTTCTGTTTCGGTGTAGGTGCTAATCGACTATGCTACTGCGGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_1_contig1_2.fastq 
@1_0_131_344_0:0:0_0:0:0_0/2
ATTCTATTGTGAGGGACGTGTTTAATACTTTCGTTAGCAAGGCACATCTACGAAAAAATGTACTTGCCATCCCCGTTAACCGCAGTAGCATAGTCGATTAGCACCTACACCGAAACAGAAACGCTATCTGGAAGGACAAGCCCCTCTCTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@1_0_158_363_0:0:0_0:0:0_1/2
CGTCGCGCGTCCAACTATGATTCTATTGTGAGGGACGTGTTTAATACTTTCGTTAGCAAGGCACATCTACGAAAAAATGTACTTGCCATCCCCGTTAACCGCAGTAGCATAGTCGATTAGCACCTACACCGAAACAGAAACGCTATCTGG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@1_0_117_314_0:0:0_0:0:0_2/2
TCGTTAGCAAGGCACATCTACGAAAAAATGTACTTGCCATCCCCGTTAACCGCAGTAGCATAGTCGATTAGCACCTACACCGAAACAGAAACGCTATCTGGAAGGACAAGCCCCTCTCTACACTCGGTACAATGAGCTGTGGATGGGAGG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_2_contig1_1.fastq 
@2_0_195_395_0:0:0_0:0:0_0/1
TAACGTTAGCCTTTGCTCACTGTCCGTCAGTAAAACTCTAGTTAGTAACGCTAGTTAAGGGCAATGCCGCCGCGGAACAGTTGTAGTTAAGTAGAAGACCTAAAGGCTGGTCCGCGAGTCACGTTTTTTCCACGGCTCGATCATTGATGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_189_381_0:0:0_0:0:0_1/1
GCTCACTGTCCGTCAGTAAAACTCTAGTTAGTAACGCTAGTTAAGGGCAATGCCGCCGCGGAACAGTTGTAGTTAAGTAGAAGACCTAAAGGCTGGTCCGCGAGTCACGTTTTTTCCACGGCTCGATCATTGATGCTACATTCCGTGATC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_9_189_0:0:0_0:0:0_2/1
AACTTAATGTATAGTTCTTGAATATCATGGGGATCCAGCCATGTGTGGACCTGAATTCCCTATGCGCTCGAACTGGGTAACACAATCAATGGGTTTTAGGTCACCGAACCCGCAGGATTGCGTATTCAAAGATTTTCTGGAACGGCCGTC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_2_contig1_2.fastq 
@2_0_195_395_0:0:0_0:0:0_0/2
TCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGAATGTAGCATCAATGATCGAGCCGTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCTTCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCTTAACTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_189_381_0:0:0_0:0:0_1/2
TGAACCTCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGAATGTAGCATCAATGATCGAGCCGTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCTTCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_9_189_0:0:0_0:0:0_2/2
TCCCTCACAATAGAATCATAGTTGGACGCGCGACGGCCGTTCCAGAAAATCTTTGAATACGCAATCCTGCGGGTTCGGTGACCTAAAACCCATTGATTGTGTTACCCAGTTCGAGCGCATAGGGAATTCAGGTCCACACATGGCTGGATC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_3_contig1_1.fastq 
@3_0_195_395_0:0:0_0:0:0_0/1
AGAGGGAAATCGTAGCCGGAAACTCCACCTTCTCATTTTTGAATATTATATTCTGGACGGACTCCTGACCCCGCTTTTAGTATCAGACCTAGTATGCAACCTTAACTCATGTCGGAGTTTAGGATTCGGAACCCATTCTCGGCCGCTAGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@3_0_189_381_0:0:0_0:0:0_1/1
GCCGGAAACTCCACCTTCTCATTTTTGAATATTATATTCTGGACGGACTCCTGACCCCGCTTTTAGTATCAGACCTAGTATGCAACCTTAACTCATGTCGGAGTTTAGGATTCGGAACCCATTCTCGGCCGCTAGTTCTGAGACATGGAT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@3_0_9_189_0:0:0_0:0:0_2/1
AGGTTAACTTCGTTGCATGAGAATCGTCGAGTATCACTTACGACGCATTCATCAATGCTTAAAGTAGCCGGTTCTGCATCGCGTGGTTAGAAGCTGATCCTCGAGCTGTAGCTCACGAAGAATGGATGTCCCGTGCTCACGGAATAACGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_3_contig1_2.fastq 
@3_0_195_395_0:0:0_0:0:0_0/2
AACTTACATTTTACGCGCTAGCTTCGCTGGAACTAATATCCATGTCTCAGAACTAGCGGCCGAGAATGGGTTCCGAATCCTAAACTCCGACATGAGTTAAGGTTGCATACTAGGTCTGATACTAAAAGCGGGGTCAGGAGTCCGTCCAGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@3_0_189_381_0:0:0_0:0:0_1/2
TATAGTAACTTACATTTTACGCGCTAGCTTCGCTGGAACTAATATCCATGTCTCAGAACTAGCGGCCGAGAATGGGTTCCGAATCCTAAACTCCGACATGAGTTAAGGTTGCATACTAGGTCTGATACTAAAAGCGGGGTCAGGAGTCCG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@3_0_9_189_0:0:0_0:0:0_2/2
AGTTTTACTGACGGACAGTGAGCAAAGGCTAACGTTATTCCGTGAGCACGGGACATCCATTCTTCGTGAGCTACAGCTCGAGGATCAGCTTCTAACCACGCGATGCAGAACCGGCTACTTTAAGCATTGATGAATGCGTCGTAAGTGATA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_4_contig1_1.fastq 
@4_0_195_395_0:0:0_0:0:0_0/1
AAGAATCACCCGTATCATCATCGCTACGTACATCTCGTACAGCAGAATTTTCTCCGACTTCTGATTCAGTAAAGACACACTTCGATCATTAGTGCGCATCGGTCCGGAAAGTCGACTAGAAGGGATGAAGCTATTAGGTCTGCTGATGAT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@4_0_189_381_0:0:0_0:0:0_1/1
TCATCATCGCTACGTACATCTCGTACAGCAGAATTTTCTCCGACTTCTGATTCAGTAAAGACACACTTCGATCATTAGTGCGCATCGGTCCGGAAAGTCGACTAGAAGGGATGAAGCTATTAGGTCTGCTGATGATTCAAAAGTGGTATA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@4_0_9_189_0:0:0_0:0:0_2/1
ACGATTGCGCACAGCTCCAACTGTTCCCTAGACATGGGGATAGGTAAACGCCACATCGTCGGAGGTAACCTAATTTGGTAATCCTCTAGTAATATTGTCTTAACCTCTCATCCGATGCTTCTTTACCACGTCCCAGGGACAGTCAGAGGG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_4_contig1_2.fastq 
@4_0_195_395_0:0:0_0:0:0_0/2
ACTATTGACATACCCCTATTCGACCAGTGCAGTAGACTATACCACTTTTGAATCATCAGCAGACCTAATAGCTTCATCCCTTCTAGTCGACTTTCCGGACCGATGCGCACTAATGATCGAAGTGTGTCTTTACTGAATCAGAAGTCGGAG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@4_0_189_381_0:0:0_0:0:0_1/2
TGTTGGACTATTGACATACCCCTATTCGACCAGTGCAGTAGACTATACCACTTTTGAATCATCAGCAGACCTAATAGCTTCATCCCTTCTAGTCGACTTTCCGGACCGATGCGCACTAATGATCGAAGTGTGTCTTTACTGAATCAGAAG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@4_0_9_189_0:0:0_0:0:0_2/2
AATGAGAAGGTGGAGTTTCCGGCTACGATTTCCCTCTGACTGTCCCTGGGACGTGGTAAAGAAGCATCGGATGAGAGGTTAAGACAATATTACTAGAGGATTACCAAATTAGGTTACCTCCGACGATGTGGCGTTTACCTATCCCCATGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_5_contig1_1.fastq 
@5_0_195_395_0:0:0_0:0:0_0/1
TAATCCCGGACCTTTACTTAAATGCCGGCATTGTCTCATCGCGCCGGTCTACGCACGAATAGGCCCGGTATCTCAAGGCACTTGAATTTGATGTAATTGGCGGAAAAGAAAGCTGAGACGCCGTATAAGAAATCAACGTGTCCTCACGCG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@5_0_189_381_0:0:0_0:0:0_1/1
TACTTAAATGCCGGCATTGTCTCATCGCGCCGGTCTACGCACGAATAGGCCCGGTATCTCAAGGCACTTGAATTTGATGTAATTGGCGGAAAAGAAAGCTGAGACGCCGTATAAGAAATCAACGTGTCCTCACGCGTCGATTGAGGCACA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@5_0_9_189_0:0:0_0:0:0_2/1
TTAGCCGTTGATCTACTAGTGACTAGGATCCGACCCTTGTCTGTTTACGCCGTGACTAGTTGCCCTCTTAGAGGTACTAAGGCCATAGGCCAGGCAAATCCCATTCACGTAAACGCAATGACCCTTTTTCGATGTACCTCATGTAAGAAT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_5_contig1_2.fastq 
@5_0_195_395_0:0:0_0:0:0_0/2
CGTCACCAGACCCTCGCCCATCTGGACTAGTAGACCGTGTGCCTCAATCGACGCGTGAGGACACGTTGATTTCTTATACGGCGTCTCAGCTTTCTTTTCCGCCAATTACATCAAATTCAAGTGCCTTGAGATACCGGGCCTATTCGTGCG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@5_0_189_381_0:0:0_0:0:0_1/2
AGTGGGCGTCACCAGACCCTCGCCCATCTGGACTAGTAGACCGTGTGCCTCAATCGACGCGTGAGGACACGTTGATTTCTTATACGGCGTCTCAGCTTTCTTTTCCGCCAATTACATCAAATTCAAGTGCCTTGAGATACCGGGCCTATT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@5_0_9_189_0:0:0_0:0:0_2/2
CGAGATGTACGTAGCGATGATGATACGGGTGATTCTTACATGAGGTACATCGAAAAAGGGTCATTGCGTTTACGTGAATGGGATTTGCCTGGCCTATGGCCTTAGTACCTCTAAGAGGGCAACTAGTCACGGCGTAAACAGACAAGGGTC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_6_contig1_1.fastq 
@6_0_195_395_0:0:0_0:0:0_0/1
GAGAGCCGCCTCGCAGGATGTGACTAATGGGGGACGCCAGTTTCAGTAGTATTCTTTGCTATAAACCTTGAGTGGCGAATCCTGGCGACAAGTGTTTTTACCTACCGAGTTTAACCGAAAACGATATGCAGTACAGGTCAAGGTTCTAGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@6_0_189_381_0:0:0_0:0:0_1/1
AGGATGTGACTAATGGGGGACGCCAGTTTCAGTAGTATTCTTTGCTATAAACCTTGAGTGGCGAATCCTGGCGACAAGTGTTTTTACCTACCGAGTTTAACCGAAAACGATATGCAGTACAGGTCAAGGTTCTAGTAGTATGGCCTGATG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@6_0_9_189_0:0:0_0:0:0_2/1
TCCTGATGTCAAGAGACGCTCCATGCATGGCACCCAGCGCATTAGCGATAAGTTCTGGAACCAAGGCCCTCCCTGCCATCATACGAGAAGGATGCGGAGTGTATACTCTCAAGGCACGCATAATTTGGCAGAGTTAGTCTACAATAATCC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_6_contig1_2.fastq 
@6_0_195_395_0:0:0_0:0:0_0/2
CGGCTCCTGTTGGGGAGTTCGAAAATAGCTTATGGGACATCAGGCCATACTACTAGAACCTTGACCTGTACTGCATATCGTTTTCGGTTAAACTCGGTAGGTAAAAACACTTGTCGCCAGGATTCGCCACTCAAGGTTTATAGCAAAGAA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@6_0_189_381_0:0:0_0:0:0_1/2
AAGTACCGGCTCCTGTTGGGGAGTTCGAAAATAGCTTATGGGACATCAGGCCATACTACTAGAACCTTGACCTGTACTGCATATCGTTTTCGGTTAAACTCGGTAGGTAAAAACACTTGTCGCCAGGATTCGCCACTCAAGGTTTATAGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@6_0_9_189_0:0:0_0:0:0_2/2
GAGACAATGCCGGCATTTAAGTAAAGGTCCGGGATTATTGTAGACTAACTCTGCCAAATTATGCGTGCCTTGAGAGTATACACTCCGCATCCTTCTCGTATGATGGCAGGGAGGGCCTTGGTTCCAGAACTTATCGCTAATGCGCTGGGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_7_contig1_1.fastq 
@7_0_195_395_0:0:0_0:0:0_0/1
CGTGCTAAGCGGGGCAGGGTTTCACCTAACGTGACGCGGGGAAGGAGGCGCGGATCACGCGTGGTCAGGTCTAACCAACTATTGTTACCGTACGCATGAGCCTTACGTAGGACGGACGACGGCCTGCAGATGCCCCCGCACTAGGCCGGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@7_0_189_381_0:0:0_0:0:0_1/1
CAGGGTTTCACCTAACGTGACGCGGGGAAGGAGGCGCGGATCACGCGTGGTCAGGTCTAACCAACTATTGTTACCGTACGCATGAGCCTTACGTAGGACGGACGACGGCCTGCAGATGCCCCCGCACTAGGCCGGAACGATAGAATCCTG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@7_0_9_189_0:0:0_0:0:0_2/1
CTGCGGTAGGAAACGGGGGCGCCATAGCTAGGCCTAATGATGCTATAGCTCCGAACAGACGGCGGTGAAACATACCGTCGTGTGCGCTGCCACCTTCAGACTAAACTCATTCGACCTTAGCCGGAGAGATCCCGTTATGCCGTCGAGAGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_7_contig1_2.fastq 
@7_0_195_395_0:0:0_0:0:0_0/2
GCATGCACTCGTTACGACAAAGTTCCTTTATTGGCTACAGGATTCTATCGTTCCGGCCTAGTGCGGGGGCATCTGCAGGCCGTCGTCCGTCCTACGTAAGGCTCATGCGTACGGTAACAATAGTTGGTTAGACCTGACCACGCGTGATCC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@7_0_189_381_0:0:0_0:0:0_1/2
GCTACTGCATGCACTCGTTACGACAAAGTTCCTTTATTGGCTACAGGATTCTATCGTTCCGGCCTAGTGCGGGGGCATCTGCAGGCCGTCGTCCGTCCTACGTAAGGCTCATGCGTACGGTAACAATAGTTGGTTAGACCTGACCACGCG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@7_0_9_189_0:0:0_0:0:0_2/2
GCGTCCCCCATTAGTCACATCCTGCGAGGCGGCTCTCGACGGCATAACGGGATCTCTCCGGCTAAGGTCGAATGAGTTTAGTCTGAAGGTGGCAGCGCACACGACGGTATGTTTCACCGCCGTCTGTTCGGAGCTATAGCATCATTAGGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_8_contig1_1.fastq 
@8_0_195_395_0:0:0_0:0:0_0/1
ACTTCGTCGGAGAGCCACAGCGGGCTATTCATATGTCTATGGCTTCGGTGGCAAGCAAGGAGCCGTGGTGATCATTGGACGGTGCTTTCTTCCTGATGCCGGTACCCTTTCCTAATGATAGATACCCGCTAGTCACCGTACACCTCCTCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@8_0_189_381_0:0:0_0:0:0_1/1
CCACAGCGGGCTATTCATATGTCTATGGCTTCGGTGGCAAGCAAGGAGCCGTGGTGATCATTGGACGGTGCTTTCTTCCTGATGCCGGTACCCTTTCCTAATGATAGATACCCGCTAGTCACCGTACACCTCCTCTATTTGTCTGTACCC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@8_0_9_189_0:0:0_0:0:0_2/1
GCCTAGTATCAATTCGGAAGCCGAGGTGCTAACGTTCAAGCCACAACACCTAGAGCGCCCCAAACCAGGAGCGTCCCAGCCTTTCATTCACCTTTTTCGGGATTGCACGTTCCTTTACCCTCAGGAAAGAGGGTTAGCATGAGACGTGCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/amplicon_8_contig1_2.fastq 
@8_0_195_395_0:0:0_0:0:0_0/2
ATCGAACACTATTAGCCGCCCTTCTTCATATTACTGTGGGTACAGACAAATAGAGGAGGTGTACGGTGACTAGCGGGTATCTATCATTAGGAAAGGGTACCGGCATCAGGAAGAAAGCACCGTCCAATGATCACCACGGCTCCTTGCTTG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@8_0_189_381_0:0:0_0:0:0_1/2
CATCCTATCGAACACTATTAGCCGCCCTTCTTCATATTACTGTGGGTACAGACAAATAGAGGAGGTGTACGGTGACTAGCGGGTATCTATCATTAGGAAAGGGTACCGGCATCAGGAAGAAAGCACCGTCCAATGATCACCACGGCTCCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@8_0_9_189_0:0:0_0:0:0_2/2
GCGTCACGTTAGGTGAAACCCTGCCCCGCTTAGCACGTCTCATGCTAACCCTCTTTCCTGAGGGTAAAGGAACGTGCAATCCCGAAAAAGGTGAATGAAAGGCTGGGACGCTCCTGGTTTGGGGCGCTCTAGGTGTTGTGGCTTGAACGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/merged_reads_1.fastq 
@2_0_195_395_0:0:0_0:0:0_0/1
TAACGTTAGCCTTTGCTCACTGTCCGTCAGTAAAACTCTAGTTAGTAACGCTAGTTAAGGGCAATGCCGCCGCGGAACAGTTGTAGTTAAGTAGAAGACCTAAAGGCTGGTCCGCGAGTCACGTTTTTTCCACGGCTCGATCATTGATGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_189_381_0:0:0_0:0:0_1/1
GCTCACTGTCCGTCAGTAAAACTCTAGTTAGTAACGCTAGTTAAGGGCAATGCCGCCGCGGAACAGTTGTAGTTAAGTAGAAGACCTAAAGGCTGGTCCGCGAGTCACGTTTTTTCCACGGCTCGATCATTGATGCTACATTCCGTGATC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_9_189_0:0:0_0:0:0_2/1
AACTTAATGTATAGTTCTTGAATATCATGGGGATCCAGCCATGTGTGGACCTGAATTCCCTATGCGCTCGAACTGGGTAACACAATCAATGGGTTTTAGGTCACCGAACCCGCAGGATTGCGTATTCAAAGATTTTCTGGAACGGCCGTC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample1/reads/merged_reads_2.fastq 
@2_0_195_395_0:0:0_0:0:0_0/2
TCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGAATGTAGCATCAATGATCGAGCCGTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCTTCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCTTAACTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_189_381_0:0:0_0:0:0_1/2
TGAACCTCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGAATGTAGCATCAATGATCGAGCCGTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCTTCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_9_189_0:0:0_0:0:0_2/2
TCCCTCACAATAGAATCATAGTTGGACGCGCGACGGCCGTTCCAGAAAATCTTTGAATACGCAATCCTGCGGGTTCGGTGACCTAAAACCCATTGATTGTGTTACCCAGTTCGAGCGCATAGGGAATTCAGGTCCACACATGGCTGGATC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/amplicons/amplicon_1.fasta 
>1_0
CCCGGCCCCTGAGTCCGAGGAGAGGGTGCTTCAGAGTATGTATACCACTGGGTAGGATAC
GGCGGAGGGCACGTCAATACGGTTCAATGCCCTACTGCATGCTCTTGTGGTTCATCTGCA
TGGAGAGGGTGGGCATGGGTGGGGGTGCTGGCCCGTGATCTGGACCTCCCATCCACAGCT
CATTGTACCGAGTGTAGAGAGGGGCTTGTCCTTCCAGATAGCGTTTCTGTTTCGGTGTAG
GTGCTAATCGACTATGCTACTGCGGTTAACGGGGATGGCAAGTACATTTTTTCGTAGATG
TGCCTTGCTAACGAAAGTATTAAACACGTCCCTCACAATAGAATCATAGTTGGACGCGCG
ACGGCCGTTCC
First lines of sample2/amplicons/amplicon_2.fasta 
>2_0
TAAACACGTCCCTCACAATAGAATCATAGTTGGACGCGCGACGGCCGTTCCAGAAAATCT
TTGAATACTCAATCCTGCGGGTTCGGTGACCTAAAACCCATTGATTGTGTTACCCAGTTC
GAGCGCGTAGGGAATTCAGGTCCACACATGGCTGGATCCCCATGATATTCAAGAACTATA
CATTAAGTTGAACCTCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGA
ATGTAGCATCAATGATCGAGCCCTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCT
TCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCTTAACTAGCGTTACTAACTAGAG
TTTTACTGACGGAAAGTGAGCAAAGGCTAACGTTATTCCGT
First lines of sample2/amplicons/amplicon_3.fasta 
>3_0
CTAACTAGAGTTTTACTGACGGAAAGTGAGCAAAGGCTAACGTTATTCCGTGAGCACGGG
ACATGCATTCTTCGTGAGCTACAGCTCGAGAATCAGCTTCTAACCAAGCGATGCAGAACC
GGCTACTTTAAGCATTGATGAATGCGTCGTAAGTGATACTCGACGATTCTCATGCAACGA
AGTTAACCTATAGTAACTTACATTTTACGCGCTAGCTTCGCTGGAACTAATATCCATGTC
TCAGAACTAGCGGCCGAGAATGGGTTCCGAATCCTAAACTCCGACATGAGTTAAGGTTGC
ATACTAGGTCTGATACTAAAAGCGGGGTCAGGAGTCCGTCCAGAATATAATATTCAAAAA
TGAGATGGTGGAGTTTCCGGCTACGATTTCCCTCTGACTGT
First lines of sample2/amplicons/amplicon_4.fasta 
>4_0
TATTCAAAAATGAGATGGTGGAGTTTCCGGCTACGATTTCCCTCTGACTGTCCCTGGGAC
GTGGTAAAGAAGCATCGGATGAGAGGTTAAGACAATATTACTAGAGGATTACCAAATTAG
GTTACCTCCGACGATGTGGCGTTTACCTATCCCCATGTCTAGGGAACAGTTGGAGCTGTG
CGCAATCGTGTTGGACTATTGACATACCCCTATTCGACCAGTGCAGTAGACTATACCACT
TTTGAATCATCAGCAGACCTAATAGCTTCATCCCTTCTAGTCGACTTTCCGGACCGATGC
GCACTAATGATCGAAGTGTGTCTTTACTGAATCAGAAGTCGGAGAAAATTCTGCTGTACG
AGATGTACGTAGCGATGATGATACGGGTGATTCTTACATGA
First lines of sample2/amplicons/amplicon_5.fasta 
>5_0
CTGCTGTACGAGATGTACGTAGCGATGATGATACGGGTGATTCTTACATGAGGTACATCG
AAAAAGGGTCATTGCGTTTACGTGAATGGGATTTGCCTGGCCTATGGCCTTAGTACCTCT
AAGAGGGCAACTAGTCACGGCGTAAACAGACAAGGGTCGGATCCTAGTCACTAGTAGATC
AACGGCTAAGTGGGCGTCACCAGACCCTCGCCCATCTGGACTAGTAGACCGTGTGCCTCA
ATCGACGCGTGAGGACACGTTGATTTCTTATACGGCGTCTCAGCTTTCTTTTCCGCCAAT
TACATCAAATTCAAGTGCCTTGAGATACCGGGCCTATTCGTGCGTAGACCGGCGCGATGA
GACAATGCCGGCATTTAAGTAAAGGTCCGGGATTATTGTAG
First lines of sample2/amplicons/amplicon_6.fasta 
>6_0
GGCGCGATGAGACAATGCCGGCATTTAAGTAAAGGTCCGGGATTATTGTAGACTAACTCT
GCCAAATTATGCGTGCCTTGAGAGTATACACTCCGCATCCTTCTCGTATGATGGCAGGGA
GGGCCTTGGTTCCAGAACTTATCGCTAATGCGCTGGGTGCCATGCATGGAGCGTCTCTTG
ACATCAGGAAGTACCGGCTCCTGTTGGGGAGTTCGAAAATAGCTTATGGGACATCAGGCC
ATACTACTAGAACCTTGACCTGTACTGCATATCGTTTTCGGTTAAACTCGGTAGGTAAAA
ACACTTGTCGCCAGGATTCGCCACTCAAGGTTTTTAGCAAAGAATACTACTGAAACTGGC
GTCCCCCATTAGTCACATCCTGCGAGGCGGCTCTCGACGGC
First lines of sample2/amplicons/amplicon_7.fasta 
>7_0
TGAAACTGGCGTCCCCCATTAGTCACATCCTGCGAGGCGGCTCTCGACGGCATAACGGGA
TCTCTCCGGCTAAGGTCGAATGAGTTTAGTCTGAAGGTGGCAGCGCACACGACGGTATGT
TTCACCGCCGTCTGTTCGGAGCTATAGCATCATTAGGCCTAGCTATGGCGCCCCCGTTTC
CTACCGCAGCTACTGCATGCACTCGTTACGACAAAGTTCCTTTATTGGCTACAGGATTCT
ATCGTTCCGGCCTAGTGCGGGGGCATCTGCAGGCCGTCGTCCGTCCTACGTAAGGCTCAT
GCGTACGGTAACAAAAGTTGGTTAGACCTGACCACGCGTGATCCGCGCCTCCTTCCCCGC
GTCACGTTAGGTGAAACCCTGCCCCGCTTAGCACGTCTCAT
First lines of sample2/amplicons/amplicon_8.fasta 
>8_0
CCTTCCCCGCGTCACGTTAGGTGAAACCCTGCCCCGCTTAGCACGTCTCATGCTAACCCT
CTTTCCTGAGGGTAAGGGAACGTGCAATCCCGAAAAAGGTGAATGAAAGGCTGGGACGCT
CCTGGTTTGGGGCGCACTAGGTGTTGTGGCTTGAACGTTAGCACCTCGGCTTCAGAATTG
ATACTAGGCATCCTATCGAACACTATTAGCCGCCCTTCTTCATATTACTGTGGGTACAGA
CAAATAGAGGAGGTGTACGGTGACTAGCGGGTATCTATCATTAGGAAAGGGTACCGGCAT
CAGGATGAAAGCACCGTCCAATGATCACCACGGCTCCTTGCTTGCCACCGAAGCCATAGA
CATATGAATAGCCAGCTGTGGCTCTCCGACGAAGTGCGCGG
First lines of sample2/amplicons/amplicon_stats.csv 
amplicon_number,primer_seq_x,primer_seq_y,ambiguous_bases,primer_start,primer_end,left_match,right_match,amplicon_length,contig_id
1,CCGGCCCCTGAGTCCGAGGAGAGGG,TAGTTGGACGCGCGACGGCCGTTCC,False,30,375,CCGGCCCCTGAGTCCGAGGAGAGGG,TAGTTGGACGCGCGACGGCCGTTCC,370,sample2
2,AAACACGTCCCTCACAATAGAATCA,TGAGCAAAGGCTAACGTTATTCCGT,False,350,725,AAACACGTCCCTCACAATAGAATCA,TGAGCAAAGGCTAACGTTATTCCGT,400,sample2
3,TAACTAGAGTTTTACTGACGGAAAG,CCGGCTACGATTTCCCTCTGACTGT,False,700,1075,TAACTAGAGTTTTACTGACGGAAAG,CCGGCTACGATTTCCCTCTGACTGT,400,sample2
4,ATTCAAAAATGAGATGGTGGAGTTT,GATGATACGGGTGATTCTTACATGA,False,1050,1425,ATTCAAAAATGAGATGGTGGAGTTT,GATGATACGGGTGATTCTTACATGA,400,sample2
5,TGCTGTACGAGATGTACGTAGCGAT,AAGTAAAGGTCCGGGATTATTGTAG,False,1400,1775,TGCTGTACGAGATGTACGTAGCGAT,AAGTAAAGGTCCGGGATTATTGTAG,400,sample2
6,GCGCGATGAGACAATGCCGGCATTT,ATCCTGCGAGGCGGCTCTCGACGGC,False,1750,2125,GCGCGATGAGACAATGCCGGCATTT,ATCCTGCGAGGCGGCTCTCGACGGC,400,sample2
7,GAAACTGGCGTCCCCCATTAGTCAC,CCCTGCCCCGCTTAGCACGTCTCAT,False,2100,2475,GAAACTGGCGTCCCCCATTAGTCAC,CCCTGCCCCGCTTAGCACGTCTCAT,400,sample2
8,CTTCCCCGCGTCACGTTAGGTGAAA,TGTGGCTCTCCGACGAAGTGCGCGG,False,2450,2825,CTTCCCCGCGTCACGTTAGGTGAAA,TGTGGCTCTCCGACGAAGTGCGCGG,400,sample2
First lines of sample2/reads/amplicon_1_contig1_1.fastq 
@1_0_131_344_0:0:0_0:0:0_0/1
GGGCATGGGTGGGGGTGCTGGCCCGTGATCTGGACCTCCCATCCACAGCTCATTGTACCGAGTGTAGAGAGGGGCTTGTCCTTCCAGATAGCGTTTCTGTTTCGGTGTAGGTGCTAATCGACTATGCTACTGCGGTTAACGGGGATGGCA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@1_0_158_363_0:0:0_0:0:0_1/1
ATCTGGACCTCCCATCCACAGCTCATTGTACCGAGTGTAGAGAGGGGCTTGTCCTTCCAGATAGCGTTTCTGTTTCGGTGTAGGTGCTAATCGACTATGCTACTGCGGTTAACGGGGATGGCAAGTACATTTTTTCGTAGATGTGCCTTG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@1_0_117_314_0:0:0_0:0:0_2/1
TGCATGGAGAGGGTGGGCATGGGTGGGGGTGCTGGCCCGTGATCTGGACCTCCCATCCACAGCTCATTGTACCGAGTGTAGAGAGGGGCTTGTCCTTCCAGATAGCGTTTCTGTTTCGGTGTAGGTGCTAATCGACTATGCTACTGCGGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_1_contig1_2.fastq 
@1_0_131_344_0:0:0_0:0:0_0/2
ATTCTATTGTGAGGGACGTGTTTAATACTTTCGTTAGCAAGGCACATCTACGAAAAAATGTACTTGCCATCCCCGTTAACCGCAGTAGCATAGTCGATTAGCACCTACACCGAAACAGAAACGCTATCTGGAAGGACAAGCCCCTCTCTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@1_0_158_363_0:0:0_0:0:0_1/2
CGTCGCGCGTCCAACTATGATTCTATTGTGAGGGACGTGTTTAATACTTTCGTTAGCAAGGCACATCTACGAAAAAATGTACTTGCCATCCCCGTTAACCGCAGTAGCATAGTCGATTAGCACCTACACCGAAACAGAAACGCTATCTGG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@1_0_117_314_0:0:0_0:0:0_2/2
TCGTTAGCAAGGCACATCTACGAAAAAATGTACTTGCCATCCCCGTTAACCGCAGTAGCATAGTCGATTAGCACCTACACCGAAACAGAAACGCTATCTGGAAGGACAAGCCCCTCTCTACACTCGGTACAATGAGCTGTGGATGGGAGG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_2_contig1_1.fastq 
@2_0_195_395_0:0:0_0:0:0_0/1
TAACGTTAGCCTTTGCTCACTTTCCGTCAGTAAAACTCTAGTTAGTAACGCTAGTTAAGGGCAATGCCGCCGCGGAACAGTTGTAGTTAAGTAGAAGACCTAAAGGCTGGTCCGCGAGTCACGTTTTTTCCAGGGCTCGATCATTGATGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_189_381_0:0:0_0:0:0_1/1
GCTCACTTTCCGTCAGTAAAACTCTAGTTAGTAACGCTAGTTAAGGGCAATGCCGCCGCGGAACAGTTGTAGTTAAGTAGAAGACCTAAAGGCTGGTCCGCGAGTCACGTTTTTTCCAGGGCTCGATCATTGATGCTACATTCCGTGATC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_9_189_0:0:0_0:0:0_2/1
AACTTAATGTATAGTTCTTGAATATCATGGGGATCCAGCCATGTGTGGACCTGAATTCCCTACGCGCTCGAACTGGGTAACACAATCAATGGGTTTTAGGTCACCGAACCCGCAGGATTGAGTATTCAAAGATTTTCTGGAACGGCCGTC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_2_contig1_2.fastq 
@2_0_195_395_0:0:0_0:0:0_0/2
TCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGAATGTAGCATCAATGATCGAGCCCTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCTTCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCTTAACTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_189_381_0:0:0_0:0:0_1/2
TGAACCTCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGAATGTAGCATCAATGATCGAGCCCTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCTTCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_9_189_0:0:0_0:0:0_2/2
TCCCTCACAATAGAATCATAGTTGGACGCGCGACGGCCGTTCCAGAAAATCTTTGAATACTCAATCCTGCGGGTTCGGTGACCTAAAACCCATTGATTGTGTTACCCAGTTCGAGCGCGTAGGGAATTCAGGTCCACACATGGCTGGATC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_3_contig1_1.fastq 
@3_0_195_395_0:0:0_0:0:0_0/1
AGAGGGAAATCGTAGCCGGAAACTCCACCATCTCATTTTTGAATATTATATTCTGGACGGACTCCTGACCCCGCTTTTAGTATCAGACCTAGTATGCAACCTTAACTCATGTCGGAGTTTAGGATTCGGAACCCATTCTCGGCCGCTAGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@3_0_189_381_0:0:0_0:0:0_1/1
GCCGGAAACTCCACCATCTCATTTTTGAATATTATATTCTGGACGGACTCCTGACCCCGCTTTTAGTATCAGACCTAGTATGCAACCTTAACTCATGTCGGAGTTTAGGATTCGGAACCCATTCTCGGCCGCTAGTTCTGAGACATGGAT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@3_0_9_189_0:0:0_0:0:0_2/1
AGGTTAACTTCGTTGCATGAGAATCGTCGAGTATCACTTACGACGCATTCATCAATGCTTAAAGTAGCCGGTTCTGCATCGCTTGGTTAGAAGCTGATTCTCGAGCTGTAGCTCACGAAGAATGCATGTCCCGTGCTCACGGAATAACGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_3_contig1_2.fastq 
@3_0_195_395_0:0:0_0:0:0_0/2
AACTTACATTTTACGCGCTAGCTTCGCTGGAACTAATATCCATGTCTCAGAACTAGCGGCCGAGAATGGGTTCCGAATCCTAAACTCCGACATGAGTTAAGGTTGCATACTAGGTCTGATACTAAAAGCGGGGTCAGGAGTCCGTCCAGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@3_0_189_381_0:0:0_0:0:0_1/2
TATAGTAACTTACATTTTACGCGCTAGCTTCGCTGGAACTAATATCCATGTCTCAGAACTAGCGGCCGAGAATGGGTTCCGAATCCTAAACTCCGACATGAGTTAAGGTTGCATACTAGGTCTGATACTAAAAGCGGGGTCAGGAGTCCG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@3_0_9_189_0:0:0_0:0:0_2/2
AGTTTTACTGACGGAAAGTGAGCAAAGGCTAACGTTATTCCGTGAGCACGGGACATGCATTCTTCGTGAGCTACAGCTCGAGAATCAGCTTCTAACCAAGCGATGCAGAACCGGCTACTTTAAGCATTGATGAATGCGTCGTAAGTGATA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_4_contig1_1.fastq 
@4_0_195_395_0:0:0_0:0:0_0/1
AAGAATCACCCGTATCATCATCGCTACGTACATCTCGTACAGCAGAATTTTCTCCGACTTCTGATTCAGTAAAGACACACTTCGATCATTAGTGCGCATCGGTCCGGAAAGTCGACTAGAAGGGATGAAGCTATTAGGTCTGCTGATGAT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@4_0_189_381_0:0:0_0:0:0_1/1
TCATCATCGCTACGTACATCTCGTACAGCAGAATTTTCTCCGACTTCTGATTCAGTAAAGACACACTTCGATCATTAGTGCGCATCGGTCCGGAAAGTCGACTAGAAGGGATGAAGCTATTAGGTCTGCTGATGATTCAAAAGTGGTATA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@4_0_9_189_0:0:0_0:0:0_2/1
ACGATTGCGCACAGCTCCAACTGTTCCCTAGACATGGGGATAGGTAAACGCCACATCGTCGGAGGTAACCTAATTTGGTAATCCTCTAGTAATATTGTCTTAACCTCTCATCCGATGCTTCTTTACCACGTCCCAGGGACAGTCAGAGGG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_4_contig1_2.fastq 
@4_0_195_395_0:0:0_0:0:0_0/2
ACTATTGACATACCCCTATTCGACCAGTGCAGTAGACTATACCACTTTTGAATCATCAGCAGACCTAATAGCTTCATCCCTTCTAGTCGACTTTCCGGACCGATGCGCACTAATGATCGAAGTGTGTCTTTACTGAATCAGAAGTCGGAG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@4_0_189_381_0:0:0_0:0:0_1/2
TGTTGGACTATTGACATACCCCTATTCGACCAGTGCAGTAGACTATACCACTTTTGAATCATCAGCAGACCTAATAGCTTCATCCCTTCTAGTCGACTTTCCGGACCGATGCGCACTAATGATCGAAGTGTGTCTTTACTGAATCAGAAG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@4_0_9_189_0:0:0_0:0:0_2/2
AATGAGATGGTGGAGTTTCCGGCTACGATTTCCCTCTGACTGTCCCTGGGACGTGGTAAAGAAGCATCGGATGAGAGGTTAAGACAATATTACTAGAGGATTACCAAATTAGGTTACCTCCGACGATGTGGCGTTTACCTATCCCCATGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_5_contig1_1.fastq 
@5_0_195_395_0:0:0_0:0:0_0/1
TAATCCCGGACCTTTACTTAAATGCCGGCATTGTCTCATCGCGCCGGTCTACGCACGAATAGGCCCGGTATCTCAAGGCACTTGAATTTGATGTAATTGGCGGAAAAGAAAGCTGAGACGCCGTATAAGAAATCAACGTGTCCTCACGCG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@5_0_189_381_0:0:0_0:0:0_1/1
TACTTAAATGCCGGCATTGTCTCATCGCGCCGGTCTACGCACGAATAGGCCCGGTATCTCAAGGCACTTGAATTTGATGTAATTGGCGGAAAAGAAAGCTGAGACGCCGTATAAGAAATCAACGTGTCCTCACGCGTCGATTGAGGCACA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@5_0_9_189_0:0:0_0:0:0_2/1
TTAGCCGTTGATCTACTAGTGACTAGGATCCGACCCTTGTCTGTTTACGCCGTGACTAGTTGCCCTCTTAGAGGTACTAAGGCCATAGGCCAGGCAAATCCCATTCACGTAAACGCAATGACCCTTTTTCGATGTACCTCATGTAAGAAT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_5_contig1_2.fastq 
@5_0_195_395_0:0:0_0:0:0_0/2
CGTCACCAGACCCTCGCCCATCTGGACTAGTAGACCGTGTGCCTCAATCGACGCGTGAGGACACGTTGATTTCTTATACGGCGTCTCAGCTTTCTTTTCCGCCAATTACATCAAATTCAAGTGCCTTGAGATACCGGGCCTATTCGTGCG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@5_0_189_381_0:0:0_0:0:0_1/2
AGTGGGCGTCACCAGACCCTCGCCCATCTGGACTAGTAGACCGTGTGCCTCAATCGACGCGTGAGGACACGTTGATTTCTTATACGGCGTCTCAGCTTTCTTTTCCGCCAATTACATCAAATTCAAGTGCCTTGAGATACCGGGCCTATT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@5_0_9_189_0:0:0_0:0:0_2/2
CGAGATGTACGTAGCGATGATGATACGGGTGATTCTTACATGAGGTACATCGAAAAAGGGTCATTGCGTTTACGTGAATGGGATTTGCCTGGCCTATGGCCTTAGTACCTCTAAGAGGGCAACTAGTCACGGCGTAAACAGACAAGGGTC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_6_contig1_1.fastq 
@6_0_195_395_0:0:0_0:0:0_0/1
GAGAGCCGCCTCGCAGGATGTGACTAATGGGGGACGCCAGTTTCAGTAGTATTCTTTGCTAAAAACCTTGAGTGGCGAATCCTGGCGACAAGTGTTTTTACCTACCGAGTTTAACCGAAAACGATATGCAGTACAGGTCAAGGTTCTAGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@6_0_189_381_0:0:0_0:0:0_1/1
AGGATGTGACTAATGGGGGACGCCAGTTTCAGTAGTATTCTTTGCTAAAAACCTTGAGTGGCGAATCCTGGCGACAAGTGTTTTTACCTACCGAGTTTAACCGAAAACGATATGCAGTACAGGTCAAGGTTCTAGTAGTATGGCCTGATG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@6_0_9_189_0:0:0_0:0:0_2/1
TCCTGATGTCAAGAGACGCTCCATGCATGGCACCCAGCGCATTAGCGATAAGTTCTGGAACCAAGGCCCTCCCTGCCATCATACGAGAAGGATGCGGAGTGTATACTCTCAAGGCACGCATAATTTGGCAGAGTTAGTCTACAATAATCC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_6_contig1_2.fastq 
@6_0_195_395_0:0:0_0:0:0_0/2
CGGCTCCTGTTGGGGAGTTCGAAAATAGCTTATGGGACATCAGGCCATACTACTAGAACCTTGACCTGTACTGCATATCGTTTTCGGTTAAACTCGGTAGGTAAAAACACTTGTCGCCAGGATTCGCCACTCAAGGTTTTTAGCAAAGAA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@6_0_189_381_0:0:0_0:0:0_1/2
AAGTACCGGCTCCTGTTGGGGAGTTCGAAAATAGCTTATGGGACATCAGGCCATACTACTAGAACCTTGACCTGTACTGCATATCGTTTTCGGTTAAACTCGGTAGGTAAAAACACTTGTCGCCAGGATTCGCCACTCAAGGTTTTTAGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@6_0_9_189_0:0:0_0:0:0_2/2
GAGACAATGCCGGCATTTAAGTAAAGGTCCGGGATTATTGTAGACTAACTCTGCCAAATTATGCGTGCCTTGAGAGTATACACTCCGCATCCTTCTCGTATGATGGCAGGGAGGGCCTTGGTTCCAGAACTTATCGCTAATGCGCTGGGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_7_contig1_1.fastq 
@7_0_195_395_0:0:0_0:0:0_0/1
CGTGCTAAGCGGGGCAGGGTTTCACCTAACGTGACGCGGGGAAGGAGGCGCGGATCACGCGTGGTCAGGTCTAACCAACTTTTGTTACCGTACGCATGAGCCTTACGTAGGACGGACGACGGCCTGCAGATGCCCCCGCACTAGGCCGGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@7_0_189_381_0:0:0_0:0:0_1/1
CAGGGTTTCACCTAACGTGACGCGGGGAAGGAGGCGCGGATCACGCGTGGTCAGGTCTAACCAACTTTTGTTACCGTACGCATGAGCCTTACGTAGGACGGACGACGGCCTGCAGATGCCCCCGCACTAGGCCGGAACGATAGAATCCTG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@7_0_9_189_0:0:0_0:0:0_2/1
CTGCGGTAGGAAACGGGGGCGCCATAGCTAGGCCTAATGATGCTATAGCTCCGAACAGACGGCGGTGAAACATACCGTCGTGTGCGCTGCCACCTTCAGACTAAACTCATTCGACCTTAGCCGGAGAGATCCCGTTATGCCGTCGAGAGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_7_contig1_2.fastq 
@7_0_195_395_0:0:0_0:0:0_0/2
GCATGCACTCGTTACGACAAAGTTCCTTTATTGGCTACAGGATTCTATCGTTCCGGCCTAGTGCGGGGGCATCTGCAGGCCGTCGTCCGTCCTACGTAAGGCTCATGCGTACGGTAACAAAAGTTGGTTAGACCTGACCACGCGTGATCC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@7_0_189_381_0:0:0_0:0:0_1/2
GCTACTGCATGCACTCGTTACGACAAAGTTCCTTTATTGGCTACAGGATTCTATCGTTCCGGCCTAGTGCGGGGGCATCTGCAGGCCGTCGTCCGTCCTACGTAAGGCTCATGCGTACGGTAACAAAAGTTGGTTAGACCTGACCACGCG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@7_0_9_189_0:0:0_0:0:0_2/2
GCGTCCCCCATTAGTCACATCCTGCGAGGCGGCTCTCGACGGCATAACGGGATCTCTCCGGCTAAGGTCGAATGAGTTTAGTCTGAAGGTGGCAGCGCACACGACGGTATGTTTCACCGCCGTCTGTTCGGAGCTATAGCATCATTAGGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_8_contig1_1.fastq 
@8_0_195_395_0:0:0_0:0:0_0/1
ACTTCGTCGGAGAGCCACAGCTGGCTATTCATATGTCTATGGCTTCGGTGGCAAGCAAGGAGCCGTGGTGATCATTGGACGGTGCTTTCATCCTGATGCCGGTACCCTTTCCTAATGATAGATACCCGCTAGTCACCGTACACCTCCTCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@8_0_189_381_0:0:0_0:0:0_1/1
CCACAGCTGGCTATTCATATGTCTATGGCTTCGGTGGCAAGCAAGGAGCCGTGGTGATCATTGGACGGTGCTTTCATCCTGATGCCGGTACCCTTTCCTAATGATAGATACCCGCTAGTCACCGTACACCTCCTCTATTTGTCTGTACCC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@8_0_9_189_0:0:0_0:0:0_2/1
GCCTAGTATCAATTCTGAAGCCGAGGTGCTAACGTTCAAGCCACAACACCTAGTGCGCCCCAAACCAGGAGCGTCCCAGCCTTTCATTCACCTTTTTCGGGATTGCACGTTCCCTTACCCTCAGGAAAGAGGGTTAGCATGAGACGTGCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/amplicon_8_contig1_2.fastq 
@8_0_195_395_0:0:0_0:0:0_0/2
ATCGAACACTATTAGCCGCCCTTCTTCATATTACTGTGGGTACAGACAAATAGAGGAGGTGTACGGTGACTAGCGGGTATCTATCATTAGGAAAGGGTACCGGCATCAGGATGAAAGCACCGTCCAATGATCACCACGGCTCCTTGCTTG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@8_0_189_381_0:0:0_0:0:0_1/2
CATCCTATCGAACACTATTAGCCGCCCTTCTTCATATTACTGTGGGTACAGACAAATAGAGGAGGTGTACGGTGACTAGCGGGTATCTATCATTAGGAAAGGGTACCGGCATCAGGATGAAAGCACCGTCCAATGATCACCACGGCTCCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@8_0_9_189_0:0:0_0:0:0_2/2
GCGTCACGTTAGGTGAAACCCTGCCCCGCTTAGCACGTCTCATGCTAACCCTCTTTCCTGAGGGTAAGGGAACGTGCAATCCCGAAAAAGGTGAATGAAAGGCTGGGACGCTCCTGGTTTGGGGCGCACTAGGTGTTGTGGCTTGAACGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/merged_reads_1.fastq 
@2_0_195_395_0:0:0_0:0:0_0/1
TAACGTTAGCCTTTGCTCACTTTCCGTCAGTAAAACTCTAGTTAGTAACGCTAGTTAAGGGCAATGCCGCCGCGGAACAGTTGTAGTTAAGTAGAAGACCTAAAGGCTGGTCCGCGAGTCACGTTTTTTCCAGGGCTCGATCATTGATGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_189_381_0:0:0_0:0:0_1/1
GCTCACTTTCCGTCAGTAAAACTCTAGTTAGTAACGCTAGTTAAGGGCAATGCCGCCGCGGAACAGTTGTAGTTAAGTAGAAGACCTAAAGGCTGGTCCGCGAGTCACGTTTTTTCCAGGGCTCGATCATTGATGCTACATTCCGTGATC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_9_189_0:0:0_0:0:0_2/1
AACTTAATGTATAGTTCTTGAATATCATGGGGATCCAGCCATGTGTGGACCTGAATTCCCTACGCGCTCGAACTGGGTAACACAATCAATGGGTTTTAGGTCACCGAACCCGCAGGATTGAGTATTCAAAGATTTTCTGGAACGGCCGTC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
First lines of sample2/reads/merged_reads_2.fastq 
@2_0_195_395_0:0:0_0:0:0_0/2
TCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGAATGTAGCATCAATGATCGAGCCCTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCTTCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCTTAACTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_189_381_0:0:0_0:0:0_1/2
TGAACCTCCAGAACACATGTTTCAGTCACGTAGTGCCATCATCGATCACGGAATGTAGCATCAATGATCGAGCCCTGGAAAAAACGTGACTCGCGGACCAGCCTTTAGGTCTTCTACTTAACTACAACTGTTCCGCGGCGGCATTGCCCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@2_0_9_189_0:0:0_0:0:0_2/2
TCCCTCACAATAGAATCATAGTTGGACGCGCGACGGCCGTTCCAGAAAATCTTTGAATACTCAATCCTGCGGGTTCGGTGACCTAAAACCCATTGATTGTGTTACCCAGTTCGAGCGCGTAGGGAATTCAGGTCCACACATGGCTGGATC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

Parameters

OptionMeaningExample valueRange
--proportionsRead proportions (sample 1, sample 2)0.7,0.30.5,0.5, 0.7,0.3, 0.8,0.2, 0.9,0.1, 0.95,0.05
--readcntReads per amplicon1001 to 5000
--maxmismatchMax mismatches in primer region10 to 5
--insert_sizeOuter distance20050 to 1000
--insert_size_sdInsert size standard deviation100 to 200
--read_lengthRead length15030 to 300
--wgsim_error_rateBase error rate0.00010 to 0.1

Ranges are the limits used for the example recipe; the program itself may accept more.

Reading the output

The example mixes two 3,000 bp genomes at 0.7 and 0.3 using a 16-line primer BED (8 amplicons). The log lists each genome with 0 ambiguous bases.

  • reads_1.fastq and reads_2.fastq (266,527 bytes each): 800 read pairs, which is 8 amplicons x 100 reads. Names look like @2_0_195_395_0:0:0_0:0:0_0/1, the wgsim format, with amplicon 2 first. Quality is I everywhere.
  • sample1/ and sample2/: amplicons/amplicon_N.fasta, amplicons/amplicon_stats.csv, per-amplicon read files and reads/merged_reads_*.fastq.
  • The stats CSV has the expected primers, the sequence found, ambiguous_bases, amplicon start and end, and length.

Counting merged reads gives 616 pairs from sample 1 and 184 from sample 2. That is 77:23 for a 70:30 request.

The primer BED has six columns: chromosome, start, end, name, pool and strand. Scheme 1 has its left primer at ref 30 55 in pool 1 and its right primer at 375 400. For amplicon 1, the stats CSV records primer_start 30, primer_end 375 and amplicon_length 370. Its left_match and right_match equal the expected primers, so no mismatch was needed. Amplicons 2 to 8 report 400 bp.

Your own runs

  • Skewed mix. --proportions 0.95,0.05. Result: 776 pairs from sample 1 and 24 from sample 2 (97:3).
  • Strict primers and more depth. --proportions 0.5,0.5 --readcnt 500 --maxmismatch 0. Result: 3,538 pairs. Sample 1 has 6 amplicons with 231 pairs each (1,386), because amplicons 3 and 4 are gone. Sample 2 keeps 8 amplicons with 269 pairs each (2,152). The 50:50 request came out as 46:54 per amplicon.
  • Your scheme. Use the reference your BED coordinates refer to. Check amplicon_stats.csv for rows where left_match or right_match differ from the primer.

Pitfalls

  • Strict mismatch silently drops amplicons. With --maxmismatch 0 two sample 1 amplicons vanished. Compare amplicon counts across samples before you read dropout as biology.
  • Realized proportions drift. Observed splits were 77:23, 97:3 and 46:54 for 70:30, 95:5 and 50:50. Count reads per sample if the exact mix matters.
  • Reference must match the BED. The BED coordinates refer to --reference. Sample genomes are searched for the primer sequences.
  • Option spelling. The README spells some options differently from the tool's help. Use --maxmismatch and --insert_size.
  • Default threads is 4. Pass --threads 1 on a small machine.

Further reading

Cite: Andersen lab. Bygul, https://github.com/andersen-lab/Bygul