CHANGES.rst
CITATION
LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
versioneer.py
doc/Makefile
doc/changes.rst
doc/colorspace.rst
doc/conf.py
doc/develop.rst
doc/guide.rst
doc/ideas.rst
doc/index.rst
doc/installation.rst
doc/recipes.rst
src/cutadapt/__init__.py
src/cutadapt/__main__.py
src/cutadapt/_align.c
src/cutadapt/_align.pyx
src/cutadapt/_qualtrim.c
src/cutadapt/_qualtrim.pyx
src/cutadapt/_seqio.c
src/cutadapt/_seqio.pyx
src/cutadapt/_version.py
src/cutadapt/adapters.py
src/cutadapt/align.py
src/cutadapt/colorspace.py
src/cutadapt/compat.py
src/cutadapt/filters.py
src/cutadapt/modifiers.py
src/cutadapt/pipeline.py
src/cutadapt/qualtrim.py
src/cutadapt/report.py
src/cutadapt/seqio.py
src/cutadapt.egg-info/PKG-INFO
src/cutadapt.egg-info/SOURCES.txt
src/cutadapt.egg-info/dependency_links.txt
src/cutadapt.egg-info/entry_points.txt
src/cutadapt.egg-info/requires.txt
src/cutadapt.egg-info/top_level.txt
tests/test_adapters.py
tests/test_align.py
tests/test_colorspace.py
tests/test_commandline.py
tests/test_filters.py
tests/test_modifiers.py
tests/test_paired.py
tests/test_qualtrim.py
tests/test_seqio.py
tests/test_trim.py
tests/utils.py
tests/cut/454.fa
tests/cut/SRR2040271_1.fastq
tests/cut/anchored-back.fasta
tests/cut/anchored.fasta
tests/cut/anchored_no_indels.fasta
tests/cut/anchored_no_indels_wildcard.fasta
tests/cut/anywhere_repeat.fastq
tests/cut/demultiplexed.first.1.fastq
tests/cut/demultiplexed.first.2.fastq
tests/cut/demultiplexed.second.1.fastq
tests/cut/demultiplexed.second.2.fastq
tests/cut/demultiplexed.unknown.1.fastq
tests/cut/demultiplexed.unknown.2.fastq
tests/cut/discard-untrimmed.fastq
tests/cut/discard.fastq
tests/cut/dos.fastq
tests/cut/empty.fastq
tests/cut/example.fa
tests/cut/examplefront.fa
tests/cut/illumina.fastq
tests/cut/illumina.info.txt
tests/cut/illumina5.fastq
tests/cut/illumina5.info.txt
tests/cut/illumina64.fastq
tests/cut/interleaved.fastq
tests/cut/issue46.fasta
tests/cut/linked-anchored.fasta
tests/cut/linked-discard-g.fasta
tests/cut/linked-discard.fasta
tests/cut/linked-not-anchored.fasta
tests/cut/linked.fasta
tests/cut/lowercase.fastq
tests/cut/lowqual.fastq
tests/cut/maxlen.fa
tests/cut/maxn0.2.fasta
tests/cut/maxn0.4.fasta
tests/cut/maxn0.fasta
tests/cut/maxn1.fasta
tests/cut/maxn2.fasta
tests/cut/minlen.fa
tests/cut/minlen.noprimer.fa
tests/cut/nextseq.fastq
tests/cut/no-trim.fastq
tests/cut/no_indels.fasta
tests/cut/overlapa.fa
tests/cut/overlapb.fa
tests/cut/paired-filterboth.1.fastq
tests/cut/paired-filterboth.2.fastq
tests/cut/paired-m27.1.fastq
tests/cut/paired-m27.2.fastq
tests/cut/paired-onlyA.1.fastq
tests/cut/paired-onlyA.2.fastq
tests/cut/paired-separate.1.fastq
tests/cut/paired-separate.2.fastq
tests/cut/paired-too-short.1.fastq
tests/cut/paired-too-short.2.fastq
tests/cut/paired-trimmed.1.fastq
tests/cut/paired-trimmed.2.fastq
tests/cut/paired-untrimmed.1.fastq
tests/cut/paired-untrimmed.2.fastq
tests/cut/paired.1.fastq
tests/cut/paired.2.fastq
tests/cut/paired.m14.1.fastq
tests/cut/paired.m14.2.fastq
tests/cut/pairedq.1.fastq
tests/cut/pairedq.2.fastq
tests/cut/pairedu.1.fastq
tests/cut/pairedu.2.fastq
tests/cut/plus.fastq
tests/cut/polya.fasta
tests/cut/rest.fa
tests/cut/restfront.fa
tests/cut/s_1_sequence.txt
tests/cut/shortened.fastq
tests/cut/small-no-trim.fasta
tests/cut/small.fasta
tests/cut/small.fastq
tests/cut/small.trimmed.fastq
tests/cut/small.untrimmed.fastq
tests/cut/solid-no-zerocap.fastq
tests/cut/solid.fasta
tests/cut/solid.fastq
tests/cut/solid5p-anchored.fasta
tests/cut/solid5p-anchored.fastq
tests/cut/solid5p-anchored.notrim.fasta
tests/cut/solid5p-anchored.notrim.fastq
tests/cut/solid5p.fasta
tests/cut/solid5p.fastq
tests/cut/solidbfast.fastq
tests/cut/solidmaq.fastq
tests/cut/solidqual.fastq
tests/cut/sra.fastq
tests/cut/stripped.fasta
tests/cut/suffix.fastq
tests/cut/trimN3.fasta
tests/cut/trimN5.fasta
tests/cut/twoadapters.fasta
tests/cut/twoadapters.first.fasta
tests/cut/twoadapters.second.fasta
tests/cut/twoadapters.unknown.fasta
tests/cut/unconditional-back.fastq
tests/cut/unconditional-both.fastq
tests/cut/unconditional-front.fastq
tests/cut/wildcard.fa
tests/cut/wildcardN.fa
tests/cut/wildcard_adapter.fa
tests/cut/wildcard_adapter_anywhere.fa
tests/data/454.fa
tests/data/E3M.fasta
tests/data/E3M.qual
tests/data/SRR2040271_1.fastq
tests/data/adapter.fasta
tests/data/anchored-back.fasta
tests/data/anchored.fasta
tests/data/anchored_no_indels.fasta
tests/data/anywhere_repeat.fastq
tests/data/dos.fastq
tests/data/empty.fastq
tests/data/example.fa
tests/data/illumina.fastq.gz
tests/data/illumina5.fastq
tests/data/illumina64.fastq
tests/data/interleaved.fastq
tests/data/issue46.fasta
tests/data/lengths.fa
tests/data/linked.fasta
tests/data/lowqual.fastq
tests/data/maxn.fasta
tests/data/multiblock.fastq.bz2
tests/data/multiblock.fastq.gz
tests/data/nextseq.fastq
tests/data/no_indels.fasta
tests/data/overlapa.fa
tests/data/overlapb.fa
tests/data/paired.1.fastq
tests/data/paired.2.fastq
tests/data/plus.fastq
tests/data/polya.fasta
tests/data/prefix-adapter.fasta
tests/data/rest.fa
tests/data/rest.txt
tests/data/restfront.txt
tests/data/s_1_sequence.txt.gz
tests/data/simple.fasta
tests/data/simple.fastq
tests/data/small.fastq
tests/data/small.fastq.bz2
tests/data/small.fastq.gz
tests/data/small.fastq.xz
tests/data/small.myownextension
tests/data/solid.csfasta
tests/data/solid.fasta
tests/data/solid.fastq
tests/data/solid.qual
tests/data/solid5p.fasta
tests/data/solid5p.fastq
tests/data/sra.fastq
tests/data/suffix-adapter.fasta
tests/data/toolong.fa
tests/data/tooshort.fa
tests/data/tooshort.noprimer.fa
tests/data/trimN3.fasta
tests/data/trimN5.fasta
tests/data/twoadapters.fasta
tests/data/wildcard.fa
tests/data/wildcardN.fa
tests/data/wildcard_adapter.fa
tests/data/withplus.fastq