├── .codecov.yml ├── .editorconfig ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature-suggestion.md ├── dependabot.yml ├── issue_template.md └── workflows │ ├── ci.yml │ └── pyinstaller.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CHANGES.rst ├── CITATION.cff ├── CONTRIBUTING.rst ├── LICENSE ├── MANIFEST.in ├── README.rst ├── doc ├── Makefile ├── _static │ ├── adapters.svg │ ├── cutadapt-logo.inkscape.svg │ ├── cutadapt-logo.png │ └── cutadapt-logo.svg ├── algorithms.rst ├── changes.rst ├── conf.py ├── develop.rst ├── guide.rst ├── ideas.rst ├── index.rst ├── installation.rst ├── recipes.rst ├── reference.rst └── requirements.txt ├── pyproject.toml ├── setup.py ├── src └── cutadapt │ ├── __init__.py │ ├── __main__.py │ ├── _align.pyi │ ├── _align.pyx │ ├── _kmer_finder.pyi │ ├── _kmer_finder.pyx │ ├── _match_tables.py │ ├── adapters.py │ ├── align.py │ ├── cli.py │ ├── expected_errors.h │ ├── files.py │ ├── info.pyi │ ├── info.pyx │ ├── json.py │ ├── kmer_heuristic.py │ ├── log.py │ ├── modifiers.py │ ├── parser.py │ ├── pipeline.py │ ├── predicates.py │ ├── qualtrim.pyi │ ├── qualtrim.pyx │ ├── report.py │ ├── runners.py │ ├── statistics.py │ ├── steps.py │ ├── tokenizer.py │ └── utils.py ├── tests ├── .gitignore ├── conftest.py ├── cut │ ├── 454.fa │ ├── SRR2040271_1.fastq │ ├── action_crop.fasta │ ├── action_lowercase.fasta │ ├── action_retain.fasta │ ├── adapterorder-ag.fasta │ ├── adapterorder-ga.fasta │ ├── adapterx.fasta │ ├── anchored-back.fasta │ ├── anchored.fasta │ ├── anchored_no_indels.fasta │ ├── anchored_no_indels_wildcard.fasta │ ├── anywhere_repeat.fastq │ ├── casava.fastq │ ├── combinatorial │ │ ├── combinatorial.A_G.1.fastq │ │ ├── combinatorial.A_G.2.fastq │ │ ├── combinatorial.A_T.1.fastq │ │ ├── combinatorial.A_T.2.fastq │ │ ├── combinatorial.A_unknown.1.fastq │ │ ├── combinatorial.A_unknown.2.fastq │ │ ├── combinatorial.C_G.1.fastq │ │ ├── combinatorial.C_G.2.fastq │ │ ├── combinatorial.C_T.1.fastq │ │ ├── combinatorial.C_T.2.fastq │ │ ├── combinatorial.C_unknown.1.fastq │ │ ├── combinatorial.C_unknown.2.fastq │ │ ├── combinatorial.unknown_G.1.fastq │ │ ├── combinatorial.unknown_G.2.fastq │ │ ├── combinatorial.unknown_T.1.fastq │ │ ├── combinatorial.unknown_T.2.fastq │ │ ├── combinatorial.unknown_unknown.1.fastq │ │ └── combinatorial.unknown_unknown.2.fastq │ ├── demultiplexed.first.1.fastq │ ├── demultiplexed.first.2.fastq │ ├── demultiplexed.second.1.fastq │ ├── demultiplexed.second.2.fastq │ ├── demultiplexed.unknown.1.fastq │ ├── demultiplexed.unknown.2.fastq │ ├── discard-untrimmed.fastq │ ├── discard.fastq │ ├── dos.fastq │ ├── dual-i1.1.fastq │ ├── dual-i1.2.fastq │ ├── dual-i2.1.fastq │ ├── dual-i2.2.fastq │ ├── dual-unknown.1.fastq │ ├── dual-unknown.2.fastq │ ├── empty.fasta │ ├── empty.fastq │ ├── example.fa │ ├── examplefront.fa │ ├── illumina.fastq │ ├── illumina.info.txt │ ├── illumina5.fastq │ ├── illumina5.info.txt │ ├── illumina64.fastq │ ├── info-rc.txt │ ├── interleaved.fastq │ ├── issue46.fasta │ ├── length-5.1.fastq │ ├── length-5.2.fastq │ ├── length5.1.fastq │ ├── length5.2.fastq │ ├── linked-anchored.fasta │ ├── linked-discard-g.fasta │ ├── linked-discard.fasta │ ├── linked-info.txt │ ├── linked-lowercase.fasta │ ├── linked-not-anchored.fasta │ ├── linked.fasta │ ├── lowercase.fastq │ ├── lowqual.fastq │ ├── lowqual.unchanged.fastq │ ├── maxee.fastq │ ├── maxlen.fa │ ├── maxn0.2.fasta │ ├── maxn0.4.fasta │ ├── maxn0.fasta │ ├── maxn1.fasta │ ├── maxn2.fasta │ ├── minlen.fa │ ├── minlen.noprimer.fa │ ├── multiprefix.fasta │ ├── multisuffix.fasta │ ├── nextseq.fastq │ ├── no-trim.fastq │ ├── no_indels.fasta │ ├── overlapb.fa │ ├── pair-adapters.1.fastq │ ├── pair-adapters.2.fastq │ ├── paired-filterboth.1.fastq │ ├── paired-filterboth.2.fastq │ ├── paired-filterfirst.1.fastq │ ├── paired-filterfirst.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-unchanged.1.fastq │ ├── paired-untrimmed.1.fastq │ ├── paired-untrimmed.2.fastq │ ├── paired.1.fastq │ ├── paired.2.fastq │ ├── paired.info1.txt │ ├── paired.info2.txt │ ├── paired.m14.1.fastq │ ├── paired.m14.2.fastq │ ├── pairedq.1.fastq │ ├── pairedq.2.fastq │ ├── pairedu.1.fastq │ ├── pairedu.2.fastq │ ├── plus.fastq │ ├── polya.1.fasta │ ├── polya.2.fasta │ ├── polya.legacy.1.fasta │ ├── rename.1.fastq │ ├── rename.2.fastq │ ├── rename.fastq │ ├── rename_comment_without_id.fastq │ ├── rest.fa │ ├── restfront.fa │ ├── revcomp-r1r2.1.fastq │ ├── revcomp-r1r2.2.fastq │ ├── revcomp-single-normalize.fastq │ ├── revcomp-single.fastq │ ├── revcomp.1.fastq │ ├── revcomp.2.fastq │ ├── s_1_sequence.txt │ ├── shortened-negative.fastq │ ├── shortened.fastq │ ├── simple.fasta │ ├── small-no-trim.fasta │ ├── small.fasta │ ├── small.fastq │ ├── small.trimmed.fastq │ ├── small.untrimmed.fastq │ ├── small_from_bam.fastq │ ├── solid-no-zerocap.fastq │ ├── solidqual.fastq │ ├── sra.fastq │ ├── stripped.fasta │ ├── suffix.fastq │ ├── trim-n.fasta │ ├── 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 │ └── xadapter.fasta ├── data │ ├── 454.fa │ ├── action_lowercase.fasta │ ├── action_retain.fasta │ ├── adapter-empty-name.fasta │ ├── adapter.fasta │ ├── adapterorder.fasta │ ├── anchored-back.fasta │ ├── anchored.fasta │ ├── anchored_no_indels.fasta │ ├── anywhere_repeat.fastq │ ├── casava.fastq │ ├── combinatorial.1.fastq │ ├── combinatorial.2.fastq │ ├── dos.fastq │ ├── dual-index.1.fastq │ ├── dual-index.2.fastq │ ├── empty.fasta │ ├── empty.fastq │ ├── example.fa │ ├── format-error.fastq │ ├── illumina.fastq.gz │ ├── illumina5.fastq │ ├── illumina64.fastq │ ├── info-rc.fasta │ ├── interleaved.fastq │ ├── issue46.fasta │ ├── lengths.fa │ ├── linked.fasta │ ├── lowqual.fastq │ ├── maxee.fastq │ ├── maxn.fasta │ ├── multi.fasta │ ├── multiblock.fastq.bz2 │ ├── multiblock.fastq.gz │ ├── nextseq.fastq │ ├── no_indels.fasta │ ├── onlycomment.fasta │ ├── overlapb.fa │ ├── paired.1.fastq │ ├── paired.2.fastq │ ├── polya.1.fasta │ ├── polya.2.fasta │ ├── prefix-adapter.fasta │ ├── rest.fa │ ├── rest.txt │ ├── restfront.txt │ ├── revcomp.1.fastq │ ├── revcomp.2.fastq │ ├── s_1_sequence.txt.gz │ ├── simple.fasta │ ├── simple.fasta.gz │ ├── simple.fastq │ ├── small.bam │ ├── small.fastq │ ├── small.fastq.bz2 │ ├── small.fastq.gz │ ├── small.fastq.xz │ ├── suffix-adapter.fasta │ ├── suffix.fastq │ ├── toolong.fa │ ├── tooshort.fa │ ├── tooshort.noprimer.fa │ ├── trim-n.fasta │ ├── 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