{"repo":"shenwei356/seqkit","free":true,"listed":false,"github":"https://github.com/shenwei356/seqkit","clone":"git clone https://github.com/shenwei356/seqkit.git","description":"A cross-platform and ultrafast toolkit for FASTA/Q file manipulation","language":"Go","stars":1589,"topics":["bioinformatics","cross-platform","fasta","fastq","golang","manipulation","sequence","tool","toolkit"],"license":"MIT","category":"dev_tool","readme_excerpt":"# SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation\n\n- [**Try SeqKit in your browser**](https://sandbox.bio/tutorials/seqkit-intro) (Tutorials and Exercises provided by [sandbox.bio](https://sandbox.bio/tutorials/seqkit-intro))\n- **Documents:** [http://bioinf.shenwei.me/seqkit](http://bioinf.shenwei.me/seqkit)\n([**Usage**](http://bioinf.shenwei.me/seqkit/usage/),\n[**FAQs**](http://bioinf.shenwei.me/seqkit/faq/),\n[**Tutorial**](http://bioinf.shenwei.me/seqkit/tutorial/),\nand \n[**Benchmark**](http://bioinf.shenwei.me/seqkit/benchmark/))\n- **Source code:** [https://github.com/shenwei356/seqkit](https://github.com/shenwei356/seqkit)\n[![GitHub stars](https://img.shields.io/github/stars/shenwei356/seqkit.svg?style=social&label=Star&?maxAge=2592000)](https://github.com/shenwei356/seqkit)\n[![license](https://img.shields.io/github/license/shenwei356/seqkit.svg?maxAge=2592000)](https://github.com/shenwei356/seqkit/blob/master/LICENSE)\n- **Latest version:** [![Latest Version](https://img.shields.io/github/release/shenwei356/seqkit.svg?style=flat?maxAge=86400)](https://github.com/shenwei356/seqkit/releases)\n[![Github Releases](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/total.svg?maxAge=3600)](http://bioinf.shenwei.me/seqkit/download/)\n[![Cross-platform](https://img.shields.io/badge/platform-any-ec2eb4.svg?style=flat)](http://bioinf.shenwei.me/seqkit/download/)\n[![Anaconda Cloud](https://anaconda.org/bioconda/seqkit/badges/version.svg)](https://anaconda.org/bioconda/seqkit)\n- **[Please cite](#citation):** [![doi](https://img.shields.io/badge/doi-10.1002%2Fimt2.191-blue.svg?style=flat)](https://doi.org/10.1002/imt2.191) [![Citation Badge](https://api.juleskreuer.eu/citation-badge.php?doi=10.1002/imt2.191)](https://doi.org/10.1002/imt2.191)\n- **Others**: [![check in Biotreasury](https://img.shields.io/badge/Biotreasury-collected-brightgreen)](https://biotreasury.rjmart.cn/#/tool?id=10081) \n\n\n\"Subcommands\n\n## Features\n\n- **Easy to install** ([download](http://bioinf.shenwei.me/seqkit/download/))\n - Providing statically linked executable binaries for multiple platforms (Linux/Windows/macOS, amd64/arm64) \n - Light weight and out-of-the-box, no dependencies, no compilation, no configuration\n - `conda install -c bioconda seqkit`\n- **Easy to use** \n - Ultrafast (see [technical-details](http://bioinf.shenwei.me/seqkit/usage/#technical-details-and-guides-for-use) and [benchmark](http://bioinf.shenwei.me/seqkit/benchmark))\n - Seamlessly parsing both FASTA and FASTQ formats\n - Supporting (`gzip`/`xz`/`zstd`/`bzip2`/`lz4` compressed) STDIN/STDOUT and input/output file, easily integrated in pipe\n - Reproducible results (configurable rand seed in `sample` and `shuffle`)\n - Supporting custom sequence ID via regular expression\n - Supporting [Bash/Zsh autocompletion](http://bioinf.shenwei.me/seqkit/download/#shell-completion)\n- **Versatile commands** ([usages and examples](http://bioinf.shenwei.me/seqkit/usage/))\n - Practical functions supported by [38 subcommands](#subcommands)\n\n\n## Installation\n\n#### Method 1: Download binaries\n\nGo to [Download Page](http://bioinf.shenwei.me/seqkit/download), where you can find download links to various platforms.\n\n#### Method 2: Install via Pixi\n\n pixi global install -c bioconda seqkit\n\n#### Method 3: Install via conda\n\n conda install -c bioconda seqkit\n\n#### Method 4: Install via homebrew\n\n brew install seqkit\n\n## Subcommands\n\n|Category |Command |Function |Input |Strand-sensitivity|Multi-threads|\n|:----------------|:-------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------|:-----------------|:------------|\n|Basic operation |[seq](https://bioinf.shenwei.me/seqkit/usage/#seq) |Transform sequences: extract ID/seq, filter by length/quality, remove gaps… |FASTA/Q | | |\n| |[stats](https://bioinf.shenwei.me/seqkit/usage/#stats) |Simple statistics: #seqs, min/max_len, N50, Q20%, Q30%… |FASTA/Q | |✓ |\n| |[subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq) |Get subsequences by region/gtf/bed, including flanking sequences |FASTA/Q |+ or/and - | |\n| |[sliding](https://bioinf.shenwei.me/seqkit/usage/#sliding) |Extract subsequences in sliding windows |FASTA/Q |+ only | |\n| |[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 - | |\n| |[translate](https://bioinf.shenwei.me/seqkit/usage/#translate) |translate DNA/RNA to protein sequence |FASTA/Q |+ or/and - | |\n| |[watch ](https://bioinf.shenwei.me/seqkit/usage/#watch ) |Monitoring and online histograms of sequence features |FASTA/Q | | |\n| |[scat ](https://bioinf.shenwei.me/seqkit/usage/#scat ) |Real time concatenation and streaming of fastx files |FASTA/Q | |✓ |\n|Format conversion|[fq2fa](https://bioinf.shenwei.me/seqkit/usage/#fq2fa) |Convert FASTQ to FASTA format |FASTQ | | |\n| |[fx2tab](https://bioinf.shenwei.me/seqkit/usage/#fx2tab) |Convert FASTA/Q to tabular format |FASTA/Q | | |\n| |[fa2fq](https://bioinf.shenwei.me/seqkit/usage/#fa2fq) |Retrieve corresponding FASTQ records by a FASTA file |FASTA/Q |+ only | |\n| |[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#tab2fx) |Convert tabular format to FASTA/Q format |TSV | | |\n| |[convert](https://bioinf.shenwei.me/seqkit/usage/#convert) |Convert FASTQ quality encoding between Sanger, Solexa and Illumina |FASTA/Q | | |\n|Searching |[grep](https://bioinf.shenwei.me/seqkit/usage/#grep) |Search sequences by ID/name/sequence/sequence motifs, mismatch allowed |FASTA/Q |+ and - |partly, -m |\n| |[locate](https://bioinf.shenwei.me/seqkit/usage/#locate) |Locate subsequences/motifs, mismatch allowed |FASTA/Q |+ and - |partly, -m |\n| |[amplicon](https://bioinf.shenwei.me/seqkit/usage/#amplicon) |Extract amplicon (or specific region around it), mismatch allowed |FASTA/Q |+ and - |partly, -m |\n| |[fish](https://bioinf.shenwei.me/seqkit/usage/#fish) |Look for short sequences in larger sequences |FASTA/Q |+ and - | |\n|Set operation |[sample](https://bioinf.shenwei.me/seqkit/usage/#sample) |Sample sequences by number or proportion |FASTA/Q | | |\n| |[sample2](https://bioinf.shenwei.me/seqkit/usage/#sample2) |Sample sequences by number or proportion (version 2) |FASTA/Q | | |\n| |[rmdup](https://bioinf.shenwei.me/seqkit/usage/#rmdup) |Remove duplicated sequences by ID/name/sequence |FASTA/Q |+ and - | |\n| |[common](https://bioinf.shenwei.me/seqkit/usage/#common) |Find common sequences of multiple files by id/name/sequence |FASTA/Q |+ and - | |\n| |[duplicate](https://bioinf.shenwei.me/seqkit/usage/#duplicate) |Duplicate sequences N times |FASTA/Q | | |\n| |[split](https://bioinf.shenwei.me/seqkit/usage/#split) |Split sequences into files by id/seq region/size/parts (mainly for FASTA) |FASTA preffered| | |\n| |[split2](https://bioinf.shenwei.me/seqkit/usage/#split2) |Split sequences into files by size/parts (FASTA, PE/SE FASTQ) |FASTA/Q | | |\n| |[head](https://bioinf.shenwei.me/seqkit/usage/#head) |print the first N FASTA/Q records, or leading records whose total length >= L |FASTA/Q | | |\n| |[head-genome](https://bioinf.shenwei.me/seqkit/usage/#head-genome) |Print sequences of the first genome with common prefixes in 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Clone it from GitHub. Paid listings live at /search."}