├── .dockerignore ├── .gitattributes ├── .gitignore ├── .pylintrc ├── .travis.yml ├── CHANGES.md ├── CITATION ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── atropos ├── __init__.py ├── _version.py ├── adapters │ ├── __init__.py │ └── sequencing_adapters.fa ├── align │ ├── __init__.py │ └── _align.pyx ├── commands │ ├── __init__.py │ ├── base.py │ ├── cli.py │ ├── detect │ │ ├── __init__.py │ │ ├── cli.py │ │ └── reports.py │ ├── error │ │ ├── __init__.py │ │ ├── cli.py │ │ └── reports.py │ ├── legacy_report.py │ ├── multicore.py │ ├── qc │ │ ├── __init__.py │ │ ├── cli.py │ │ └── reports.py │ ├── reports.py │ ├── stats.py │ └── trim │ │ ├── __init__.py │ │ ├── _qualtrim.pyx │ │ ├── cli.py │ │ ├── filters.py │ │ ├── modifiers.py │ │ ├── multicore.py │ │ ├── qualtrim.py │ │ ├── reports.py │ │ └── writers.py ├── io │ ├── __init__.py │ ├── _seqio.pyx │ ├── compression.py │ ├── progress.py │ └── seqio.py └── util │ ├── __init__.py │ └── colorspace.py ├── bin ├── _preamble.py └── atropos ├── doc ├── Makefile ├── _static │ ├── adapters.svg │ └── logo.svg ├── colorspace.rst ├── conf.py ├── developers.rst ├── guide.rst ├── index.rst ├── installation.rst ├── logo.ai └── recipes.rst ├── meta.yaml ├── paper ├── README.md ├── containers │ ├── README.md │ ├── data │ │ ├── DataSets.xlsx │ │ ├── README.md │ │ ├── hg37 │ │ │ ├── bwa-index │ │ │ │ ├── Dockerfile │ │ │ │ └── build.sh │ │ │ ├── bwameth-index │ │ │ │ ├── Dockerfile │ │ │ │ └── build.sh │ │ │ ├── reference │ │ │ │ ├── Dockerfile │ │ │ │ └── build.sh │ │ │ └── star-index │ │ │ │ ├── Dockerfile │ │ │ │ └── build.sh │ │ ├── hg38 │ │ │ ├── bwa-index │ │ │ │ ├── Dockerfile │ │ │ │ └── build.sh │ │ │ ├── bwameth-index │ │ │ │ ├── Dockerfile │ │ │ │ └── build.sh │ │ │ ├── reference │ │ │ │ ├── Dockerfile │ │ │ │ └── build.sh │ │ │ └── star-index │ │ │ │ ├── Dockerfile │ │ │ │ └── build.sh │ │ ├── rna │ │ │ ├── Dockerfile │ │ │ └── build.sh │ │ ├── simulated │ │ │ ├── Dockerfile │ │ │ ├── adjust_error_profiles.R │ │ │ ├── art_profiles.txt │ │ │ ├── art_profiles │ │ │ │ ├── HiSeq2500L125R1_001.txt │ │ │ │ ├── HiSeq2500L125R1_005.txt │ │ │ │ ├── HiSeq2500L125R1_01.txt │ │ │ │ ├── HiSeq2500L125R2_001.txt │ │ │ │ ├── HiSeq2500L125R2_005.txt │ │ │ │ └── HiSeq2500L125R2_01.txt │ │ │ └── build.sh │ │ └── wgbs │ │ │ ├── Dockerfile │ │ │ └── build.sh │ ├── docker2singularity.sh │ ├── paper_containers.txt │ └── tools │ │ ├── README.md │ │ ├── adapter-removal │ │ ├── Dockerfile │ │ └── adapter-removal.cwl │ │ ├── art │ │ ├── Dockerfile │ │ ├── art_illumina_src151-adapter-enabled.tar.gz │ │ └── art_illumina_src151.tar.gz │ │ ├── atropos-paper-analysis │ │ ├── Dockerfile │ │ └── fastq-dump-wrapper.sh │ │ ├── atropos-paper │ │ ├── Dockerfile │ │ └── atropos.cwl │ │ ├── bwa │ │ ├── Dockerfile │ │ ├── README.md │ │ ├── bwamem.cwl │ │ └── bwameth.cwl │ │ ├── cutadapt │ │ ├── Dockerfile │ │ └── cutadapt.cwl │ │ ├── fastp │ │ ├── Dockerfile │ │ └── fastp.cwl │ │ ├── python-bash │ │ └── Dockerfile │ │ ├── seqpurge │ │ ├── Dockerfile │ │ └── seqpurge.cwl │ │ ├── skewer │ │ ├── Dockerfile │ │ └── skewer.cwl │ │ ├── star │ │ ├── Dockerfile │ │ ├── README.md │ │ └── star.cwl │ │ └── tool-names.txt ├── manuscript │ ├── README.md │ ├── citations.bib │ ├── main │ │ ├── figures │ │ │ ├── Figure1.graffle │ │ │ ├── Figure1.pdf │ │ │ ├── Figure2.pdf │ │ │ ├── Figure3.pdf │ │ │ ├── Figure4.pdf │ │ │ └── Figure5.pdf │ │ └── tex │ │ │ ├── datasets_table.tex │ │ │ ├── main.tex │ │ │ └── simulated_accuracy_table.tex │ ├── pdfs │ │ ├── manuscript.pdf │ │ ├── response.pdf │ │ └── supplement.pdf │ ├── supplement │ │ ├── figures │ │ │ ├── FigureS1.pdf │ │ │ ├── FigureS2.pdf │ │ │ └── FigureS3.pdf │ │ └── tex │ │ │ ├── TableS1.tex │ │ │ ├── TableS2.tex │ │ │ ├── TableS3.tex │ │ │ ├── TableS4.tex │ │ │ ├── TableS5.tex │ │ │ ├── TableS6.tex │ │ │ └── main.tex │ └── wlpeerj.cls └── workflow │ ├── bin │ ├── common.py │ ├── compute_real_effectiveness.py │ ├── compute_simulated_accuracy.py │ ├── job_memory_table.tex │ ├── parse_gtime.py │ ├── parse_machine.py │ ├── parse_slurm_job.py │ ├── performance_table.tex │ ├── show_job_info.py │ ├── show_performance.py │ ├── show_rnaseq_effectiveness.py │ ├── show_simulated_accuracy.py │ ├── show_wgbs_effectiveness.py │ ├── simulated_accuracy_table.tex │ └── summarize_slurm_job.sh │ ├── extra │ ├── estimate_real_data_metrics.py │ ├── fastq_base_hist.py │ └── perftest.py │ ├── nextflow.config │ ├── rnaseq.nf │ ├── run-workflows.sh │ ├── simulated.nf │ └── wgbs.nf ├── pytest.ini ├── setup.cfg ├── setup.py ├── tests ├── .gitignore ├── __init__.py ├── cut │ ├── 454.fa │ ├── SRR2040662_trimmed.fq │ ├── anchored-back.fasta │ ├── anchored.fasta │ ├── anchored_no_indels.fasta │ ├── anchored_no_indels_wildcard.fasta │ ├── anywhere_repeat.fastq │ ├── back_repeat.1.fastq │ ├── back_repeat.2.fastq │ ├── discard-untrimmed.fastq │ ├── discard.fastq │ ├── dos.fastq │ ├── empty.fastq │ ├── empty.fastq.gz │ ├── example.fa │ ├── examplefront.fa │ ├── highq.fastq │ ├── illumina.fastq │ ├── illumina.info.txt │ ├── illumina5.fastq │ ├── illumina5.info.txt │ ├── illumina64.fastq │ ├── insert.1.fastq │ ├── insert.2.fastq │ ├── interleaved.fastq │ ├── issue46.fasta │ ├── issue68.1.fq │ ├── issue68.2.fq │ ├── linked.fasta │ ├── lowercase.fastq │ ├── lowq.fastq │ ├── lowqual.fastq │ ├── maxlen.fa │ ├── maxn0.2.fasta │ ├── maxn0.4.fasta │ ├── maxn0.fasta │ ├── maxn1.fasta │ ├── maxn2.fasta │ ├── minlen.fa │ ├── minlen.noprimer.fa │ ├── nextseq.fastq │ ├── no-trim.fastq │ ├── no_indels.fasta │ ├── overlapa.fa │ ├── overlapb.fa │ ├── paired-filterboth.1.fastq │ ├── paired-filterboth.2.fastq │ ├── paired-filterboth_adapter.1.fastq │ ├── paired-filterboth_adapter.2.fastq │ ├── paired-filterboth_insert.1.fastq │ ├── paired-filterboth_insert.2.fastq │ ├── paired-m27.1.fastq │ ├── paired-m27.2.fastq │ ├── paired-onlyA.1.fastq │ ├── paired-onlyA.2.fastq │ ├── paired-separate.1.fastq │ ├── paired-separate.2.fastq │ ├── paired-too-short.1.fastq │ ├── paired-too-short.2.fastq │ ├── paired-trimmed.1.fastq │ ├── paired-trimmed.2.fastq │ ├── paired-untrimmed.1.fastq │ ├── paired-untrimmed.2.fastq │ ├── paired.1.fastq │ ├── paired.2.fastq │ ├── paired.m14.1.fastq │ ├── paired.m14.2.fastq │ ├── paired_adapter.1.fastq │ ├── paired_adapter.2.fastq │ ├── paired_bis1_adapter.1.fastq │ ├── paired_bis1_adapter.2.fastq │ ├── paired_bis1_insert.1.fastq │ ├── paired_bis1_insert.2.fastq │ ├── paired_bis2_adapter.1.fastq │ ├── paired_bis2_adapter.2.fastq │ ├── paired_bis2_insert.1.fastq │ ├── paired_bis2_insert.2.fastq │ ├── paired_insert.1.fastq │ ├── paired_insert.2.fastq │ ├── pairedq.1.fastq │ ├── pairedq.2.fastq │ ├── pairedu.1.fastq │ ├── pairedu.2.fastq │ ├── plus.fastq │ ├── polya.fasta │ ├── rest.fa │ ├── restfront.fa │ ├── s_1_sequence.txt │ ├── small.fasta │ ├── small.fastq │ ├── small.trimmed.fastq │ ├── small.untrimmed.fastq │ ├── small_mincut1.fastq │ ├── small_mincut2.fastq │ ├── small_mincut3.fastq │ ├── solid-no-zerocap.fastq │ ├── solid.fasta │ ├── solid.fastq │ ├── solid5p-anchored.fasta │ ├── solid5p-anchored.fastq │ ├── solid5p-anchored.notrim.fasta │ ├── solid5p-anchored.notrim.fastq │ ├── solid5p.fasta │ ├── solid5p.fastq │ ├── solidbfast.fastq │ ├── solidmaq.fastq │ ├── solidqual.fastq │ ├── sra.fastq │ ├── stripped.fasta │ ├── suffix.fastq │ ├── trimN3.fasta │ ├── trimN5.fasta │ ├── twoadapters.fasta │ ├── twoadapters.first.fasta │ ├── twoadapters.second.fasta │ ├── twoadapters.unknown.fasta │ ├── unconditional-back.fastq │ ├── unconditional-both.fastq │ ├── unconditional-front.fastq │ ├── wildcard.fa │ ├── wildcardN.fa │ ├── wildcard_adapter.fa │ └── wildcard_adapter_anywhere.fa ├── data │ ├── 454.fa │ ├── E3M.fasta │ ├── E3M.qual │ ├── adapter.fasta │ ├── anchored-back.fasta │ ├── anchored.fasta │ ├── anchored_no_indels.fasta │ ├── anywhere_repeat.fastq │ ├── back_repeat.1.fastq │ ├── back_repeat.2.fastq │ ├── bad_bases.fq │ ├── big.1.fq │ ├── big.2.fq │ ├── dos.fastq │ ├── empty.fastq │ ├── example.fa │ ├── highq.fastq │ ├── illumina.fastq.gz │ ├── illumina5.fastq │ ├── illumina64.fastq │ ├── insert.1.fastq │ ├── insert.2.fastq │ ├── interleaved.fastq │ ├── issue46.fasta │ ├── issue68.1.fq │ ├── issue68.2.fq │ ├── lengths.fa │ ├── linked.fasta │ ├── lowq.fastq │ ├── lowqual.fastq │ ├── maxn.fasta │ ├── multiblock.fastq.gz │ ├── nextseq.fastq │ ├── no_indels.fasta │ ├── overlapa.fa │ ├── overlapb.fa │ ├── paired.1.fastq │ ├── paired.2.fastq │ ├── paired_bis_adapter.1.fastq │ ├── paired_bis_adapter.2.fastq │ ├── paired_bis_insert.1.fastq │ ├── paired_bis_insert.2.fastq │ ├── plus.fastq │ ├── polya.fasta │ ├── prefix-adapter.fasta │ ├── rest.fa │ ├── rest.txt │ ├── restfront.txt │ ├── s_1_sequence.txt.gz │ ├── simple.fasta │ ├── simple.fastq │ ├── small.fastq │ ├── small.fastq.bz2 │ ├── small.fastq.gz │ ├── small.fastq.xz │ ├── small.myownextension │ ├── solid.csfasta 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