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‎doc/docs/index.md

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# SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
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- **Documents:** [http://bioinf.shenwei.me/seqkit](http://bioinf.shenwei.me/seqkit)
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([**Usage**](http://bioinf.shenwei.me/seqkit/usage/),
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[**FAQ**](http://bioinf.shenwei.me/seqkit/faq/),
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[**Tutorial**](http://bioinf.shenwei.me/seqkit/tutorial/),
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and
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[**Benchmark**](http://bioinf.shenwei.me/seqkit/benchmark/))
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- **Source code:** [https://github.com/shenwei356/seqkit](https://github.com/shenwei356/seqkit)
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[![GitHub stars](https://img.shields.io/github/stars/shenwei356/seqkit.svg?style=social&label=Star&?maxAge=2592000)](https://github.com/shenwei356/seqkit)
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[![license](https://img.shields.io/github/license/shenwei356/seqkit.svg?maxAge=2592000)](https://github.com/shenwei356/seqkit/blob/master/LICENSE)
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- **Latest version:** [![Latest Version](https://img.shields.io/github/release/shenwei356/seqkit.svg?style=flat?maxAge=86400)](https://github.com/shenwei356/seqkit/releases)
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[![Github Releases](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/total.svg?maxAge=3600)](http://bioinf.shenwei.me/seqkit/download/)
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[![Cross-platform](https://img.shields.io/badge/platform-any-ec2eb4.svg?style=flat)](http://bioinf.shenwei.me/seqkit/download/)
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[![Anaconda Cloud](https://anaconda.org/bioconda/seqkit/badges/version.svg)](https://anaconda.org/bioconda/seqkit)
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- **[Please cite](#citation):** [![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pone.0163962-blue.svg?style=flat)](https://doi.org/10.1371/journal.pone.0163962)
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[![Citation Badge](https://api.juleskreuer.eu/citation-badge.php?doi=10.1371/journal.pone.0163962)](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=wHF3Lm8AAAAJ&citation_for_view=wHF3Lm8AAAAJ:zYLM7Y9cAGgC)
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- **Others**: [![check in Biotreasury](https://img.shields.io/badge/Biotreasury-collected-brightgreen)](https://biotreasury.rjmart.cn/#/tool?id=10081)
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## Features
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- **Easy to install** ([download](http://bioinf.shenwei.me/seqkit/download/))
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- Providing statically linked executable binaries for multiple platforms (Linux/Windows/macOS, amd64/arm64)
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- Light weight and out-of-the-box, no dependencies, no compilation, no configuration
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- `conda install -c bioconda seqkit`
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- **Easy to use**
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- Ultrafast (see [technical-details](http://bioinf.shenwei.me/seqkit/usage/#technical-details-and-guides-for-use) and [benchmark](http://bioinf.shenwei.me/seqkit/benchmark))
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- Seamlessly parsing both FASTA and FASTQ formats
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- Supporting (`gzip`/`xz`/`zstd`/`bzip2` compressed) STDIN/STDOUT and input/output file, easily integrated in pipe
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- Reproducible results (configurable rand seed in `sample` and `shuffle`)
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- Supporting custom sequence ID via regular expression
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- Supporting [Bash/Zsh autocompletion](http://bioinf.shenwei.me/seqkit/download/#shell-completion)
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- **Versatile commands** ([usages and examples](http://bioinf.shenwei.me/seqkit/usage/))
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- Practical functions supported by [38 subcommands](#subcommands)
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## Installation
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Go to [Download Page](http://bioinf.shenwei.me/seqkit/download) for more download options and changelogs, or
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install via conda:
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conda install -c bioconda seqkit
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## Subcommands
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|Category |Command |Function |Input |Strand-sensitivity|Multi-threads|
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|:----------------|:-------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------|:-----------------|:------------|
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|Basic operation |[seq](https://bioinf.shenwei.me/seqkit/usage/#seq) |Transform sequences: extract ID/seq, filter by length/quality, remove gaps… |FASTA/Q | | |
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| |[stats](https://bioinf.shenwei.me/seqkit/usage/#stats) |Simple statistics: #seqs, min/max_len, N50, Q20%, Q30%… |FASTA/Q | |✓ |
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| |[subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq) |Get subsequences by region/gtf/bed, including flanking sequences |FASTA/Q |+ or/and - | |
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| |[sliding](https://bioinf.shenwei.me/seqkit/usage/#sliding) |Extract subsequences in sliding windows |FASTA/Q |+ only | |
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| |[faidx](https://bioinf.shenwei.me/seqkit/usage/#faidx) |Create the FASTA index file and extract subsequences (with more features than samtools faidx)|FASTA |+ or/and - | |
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| |[translate](https://bioinf.shenwei.me/seqkit/usage/#translate) |translate DNA/RNA to protein sequence |FASTA/Q |+ or/and - | |
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| |[watch ](https://bioinf.shenwei.me/seqkit/usage/#watch ) |Monitoring and online histograms of sequence features |FASTA/Q | | |
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| |[scat ](https://bioinf.shenwei.me/seqkit/usage/#scat ) |Real time concatenation and streaming of fastx files |FASTA/Q | |✓ |
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|Format conversion|[fq2fa](https://bioinf.shenwei.me/seqkit/usage/#fq2fa) |Convert FASTQ to FASTA format |FASTQ | | |
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| |[fx2tab](https://bioinf.shenwei.me/seqkit/usage/#fx2tab) |Convert FASTA/Q to tabular format |FASTA/Q | | |
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| |[fa2fq](https://bioinf.shenwei.me/seqkit/usage/#fa2fq) |Retrieve corresponding FASTQ records by a FASTA file |FASTA/Q |+ only | |
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| |[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#tab2fx) |Convert tabular format to FASTA/Q format |TSV | | |
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| |[convert](https://bioinf.shenwei.me/seqkit/usage/#convert) |Convert FASTQ quality encoding between Sanger, Solexa and Illumina |FASTA/Q | | |
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|Searching |[grep](https://bioinf.shenwei.me/seqkit/usage/#grep) |Search sequences by ID/name/sequence/sequence motifs, mismatch allowed |FASTA/Q |+ and - |partly, -m |
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| |[locate](https://bioinf.shenwei.me/seqkit/usage/#locate) |Locate subsequences/motifs, mismatch allowed |FASTA/Q |+ and - |partly, -m |
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| |[amplicon](https://bioinf.shenwei.me/seqkit/usage/#amplicon) |Extract amplicon (or specific region around it), mismatch allowed |FASTA/Q |+ and - |partly, -m |
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| |[fish](https://bioinf.shenwei.me/seqkit/usage/#fish) |Look for short sequences in larger sequences |FASTA/Q |+ and - | |
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|Set operation |[sample](https://bioinf.shenwei.me/seqkit/usage/#sample) |Sample sequences by number or proportion |FASTA/Q | | |
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| |[rmdup](https://bioinf.shenwei.me/seqkit/usage/#rmdup) |Remove duplicated sequences by ID/name/sequence |FASTA/Q |+ and - | |
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| |[common](https://bioinf.shenwei.me/seqkit/usage/#common) |Find common sequences of multiple files by id/name/sequence |FASTA/Q |+ and - | |
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| |[duplicate](https://bioinf.shenwei.me/seqkit/usage/#duplicate) |Duplicate sequences N times |FASTA/Q | | |
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| |[split](https://bioinf.shenwei.me/seqkit/usage/#split) |Split sequences into files by id/seq region/size/parts (mainly for FASTA) |FASTA preffered| | |
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| |[split2](https://bioinf.shenwei.me/seqkit/usage/#split2) |Split sequences into files by size/parts (FASTA, PE/SE FASTQ) |FASTA/Q | | |
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| |[head](https://bioinf.shenwei.me/seqkit/usage/#head) |Print first N FASTA/Q records |FASTA/Q | | |
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| |[head-genome](https://bioinf.shenwei.me/seqkit/usage/#head-genome) |Print sequences of the first genome with common prefixes in name |FASTA/Q | | |
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| |[range](https://bioinf.shenwei.me/seqkit/usage/#range) |Print FASTA/Q records in a range (start:end) |FASTA/Q | | |
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| |[pair](https://bioinf.shenwei.me/seqkit/usage/#pair) |Patch up paired-end reads from two fastq files |FASTA/Q | | |
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|Edit |[replace](https://bioinf.shenwei.me/seqkit/usage/#replace) |Replace name/sequence by regular expression |FASTA/Q |+ only | |
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| |[rename](https://bioinf.shenwei.me/seqkit/usage/#rename) |Rename duplicated IDs |FASTA/Q | | |
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| |[concat](https://bioinf.shenwei.me/seqkit/usage/#concat) |Concatenate sequences with same ID from multiple files |FASTA/Q |+ only | |
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| |[restart](https://bioinf.shenwei.me/seqkit/usage/#restart) |Reset start position for circular genome |FASTA/Q |+ only | |
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| |[mutate](https://bioinf.shenwei.me/seqkit/usage/#mutate) |Edit sequence (point mutation, insertion, deletion) |FASTA/Q |+ only | |
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| |[sana](https://bioinf.shenwei.me/seqkit/usage/#sana) |Sanitize broken single line FASTQ files |FASTQ | | |
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|Ordering |[sort](https://bioinf.shenwei.me/seqkit/usage/#sort) |Sort sequences by id/name/sequence/length |FASTA preffered| | |
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| |[shuffle](https://bioinf.shenwei.me/seqkit/usage/#shuffle) |Shuffle sequences |FASTA preffered| | |
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|BAM processing |[bam](https://bioinf.shenwei.me/seqkit/usage/#bam) |Monitoring and online histograms of BAM record features |BAM | | |
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|Miscellaneous |[sum](https://bioinf.shenwei.me/seqkit/usage/#sum) |Compute message digest for all sequences in FASTA/Q files |FASTA/Q | |✓ |
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| |[merge-slides](https://bioinf.shenwei.me/seqkit/usage/#merge-slides)|Merge sliding windows generated from seqkit sliding |TSV | |
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Notes:
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- Strand-sensitivity:
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- `+ only`: only processing on the positive/forward strand.
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- `+ and -`: searching on both strands.
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- `+ or/and -`: depends on users' flags/options/arguments.
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- Multiple-threads: Using the default 4 threads is fast enough for most commands, some commands can benefit from extra threads.
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## Citation
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**W Shen**, S Le, Y Li\*, F Hu\*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
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***PLOS ONE***. [doi:10.1371/journal.pone.0163962](https://doi.org/10.1371/journal.pone.0163962).
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<span class="__dimensions_badge_embed__" data-doi="10.1371/journal.pone.0163962" data-style="small_rectangle"></span>
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## Contributors
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- [Wei Shen](https://github.com/shenwei356)
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- [Botond Sipos](https://github.com/botond-sipos): `bam`, `scat`, `fish`, `sana`, `watch`.
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- [others](https://github.com/shenwei356/seqkit/graphs/contributors)
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## Acknowledgements
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We thank [Lei Zhang](https://github.com/jameslz) for testing SeqKit,
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and also thank [Jim Hester](https://github.com/jimhester/),
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author of [fasta_utilities](https://github.com/jimhester/fasta_utilities),
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for advice on early performance improvements of for FASTA parsing
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and [Brian Bushnell](https://twitter.com/BBToolsBio),
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author of [BBMaps](https://sourceforge.net/projects/bbmap/),
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for advice on naming SeqKit and adding accuracy evaluation in benchmarks.
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We also thank Nicholas C. Wu from the Scripps Research Institute,
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USA for commenting on the manuscript
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and [Guangchuang Yu](http://guangchuangyu.github.io/)
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from State Key Laboratory of Emerging Infectious Diseases,
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The University of Hong Kong, HK for advice on the manuscript.
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We thank [Li Peng](https://github.com/penglbio) for reporting many bugs.
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We appreciate [Klaus Post](https://github.com/klauspost) for his fantastic packages (
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[compress](https://github.com/klauspost/compress) and [pgzip](https://github.com/klauspost/pgzip)
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) which accelerate gzip file reading and writing.
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## Contact
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[Create an issue](https://github.com/shenwei356/seqkit/issues) to report bugs,
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propose new functions or ask for help.
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## License
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[MIT License](https://github.com/shenwei356/seqkit/blob/master/LICENSE)
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## Starchart
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<img src="https://starchart.cc/shenwei356/seqkit.svg" alt="Stargazers over time" style="max-width: 100%">
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‎doc/docs/usage.md

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``` text
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get subsequences by region/gtf/bed, including flanking sequences.
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Attention:
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1. Use "seqkit grep" for extract subsets of sequences.
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"seqtk subseq seqs.fasta id.txt" equals to
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17. AvgQual average quality
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18. GC(%) percentage of GC content
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1. Sequence length metrics (sum_len, min_len, avg_len, max_len, Q1, Q2, Q3)
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count the number of gaps or spaces. You can remove them with "seqkit seq -g":
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seqkit seq -g input.fasta | seqkit stats
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compute message digest for all sequences in FASTA/Q files
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seqkit faidx seqs.fasta -l IDs.txt
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edit sequence (point mutation, insertion, deletion)
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‎seqkit/cmd/amplicon.go

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You can increase the value of "-j/--threads" to accelerate processing.

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