# seqkit
**Repository Path**: all_create_code/seqkit
## Basic Information
- **Project Name**: seqkit
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No
## Statistics
- **Stars**: 0
- **Forks**: 0
- **Created**: 2020-10-30
- **Last Updated**: 2022-06-07
## Categories & Tags
**Categories**: Uncategorized
**Tags**: None
## README
# SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
- **Documents:** [http://bioinf.shenwei.me/seqkit](http://bioinf.shenwei.me/seqkit)
([**Usage**](http://bioinf.shenwei.me/seqkit/usage/),
[**FAQ**](http://bioinf.shenwei.me/seqkit/faq/),
[**Tutorial**](http://bioinf.shenwei.me/seqkit/tutorial/),
and
[**Benchmark**](http://bioinf.shenwei.me/seqkit/benchmark/))
- **Source code:** [https://github.com/shenwei356/seqkit](https://github.com/shenwei356/seqkit)
[](https://github.com/shenwei356/seqkit)
[](https://github.com/shenwei356/seqkit/blob/master/LICENSE)
[](https://travis-ci.org/shenwei356/seqkit)
- **Latest version:** [](https://github.com/shenwei356/seqkit/releases)
[](http://bioinf.shenwei.me/seqkit/download/)
[](http://bioinf.shenwei.me/seqkit/download/)
[](https://anaconda.org/bioconda/seqkit)
- **[Please cite](#citation):** [](https://doi.org/10.1371/journal.pone.0163962)
- **Others**: [](https://biotreasury.rjmart.cn/#/tool?id=10081)
## Features
- **Easy to install** ([download](http://bioinf.shenwei.me/seqkit/download/))
- Providing statically linked executable binaries for multiple platforms (Linux/Windows/macOS, amd64/arm64)
- Light weight and out-of-the-box, no dependencies, no compilation, no configuration
- **Easy to use**
- Ultrafast (see [technical-details](http://bioinf.shenwei.me/seqkit/usage/#technical-details-and-guides-for-use) and [benchmark](http://bioinf.shenwei.me/seqkit/benchmark))
- Seamlessly parsing both FASTA and FASTQ formats
- Supporting (`gzip`/`xz`/`zstd` compressed) STDIN/STDOUT and input/output file, easily integrated in pipe
- Reproducible results (configurable rand seed in `sample` and `shuffle`)
- Supporting custom sequence ID via regular expression
- Supporting [Bash/Zsh completion](http://bioinf.shenwei.me/seqkit/download/#shell-completion)
- **Versatile commands** ([usages and examples](http://bioinf.shenwei.me/seqkit/usage/))
- Practical functions supported by [37 subcommands](#subcommands)
## Installation
Go to [Download Page](http://bioinf.shenwei.me/seqkit/download) for more download options and changelogs, or
install via conda:
conda install -c bioconda seqkit
## Subcommands
|category |command |function |input |strand-sensitivity|multi-threads|popularity |
|:----------------|:------------------------------------------------------------------|:---------------------------------------------------------------------------------------|:--------------|:-----------------|:------------|:--------------|
|basic |[seq](https://bioinf.shenwei.me/seqkit/usage/#seq) |transform sequences: extract ID/seq, filter by length/quality, remove gaps… |FASTA/Q | | |★★★★★ |
| |[stats](https://bioinf.shenwei.me/seqkit/usage/#stats) |simple statistics: #seqs, min/max_len, N50, Q20%, Q30%… |FASTA/Q | |✓ |★★★★★ |
| |[sum](https://bioinf.shenwei.me/seqkit/usage/#sum) |compute message digest for all sequences in FASTA/Q files |FASTA/Q |+ or both |✓ | |
| |[subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq) |extract subsequences or flanking sequences by region/gtf/bed, |FASTA/Q |+ or/and - | |★★★ |
| |[sliding](https://bioinf.shenwei.me/seqkit/usage/#sliding) |extract subsequences in sliding windows |FASTA/Q |+ only | |★★ |
| |[faidx](https://bioinf.shenwei.me/seqkit/usage/#faidx) |create FASTA index file and extract subsequence (with more features than samtools faidx)|FASTA |+ or/and - | | |
| |[watch ](https://bioinf.shenwei.me/seqkit/usage/#watch ) |monitoring and online histograms of sequence features |FASTA/Q | | | |
| |[sana](https://bioinf.shenwei.me/seqkit/usage/#sana) |sanitize broken single line FASTQ files |FASTQ | | | |
| |[scat ](https://bioinf.shenwei.me/seqkit/usage/#scat ) |real time concatenation and streaming of fastx files |FASTA/Q | |✓ | |
|format conversion|[fq2fa](https://bioinf.shenwei.me/seqkit/usage/#fq2fa) |convert FASTQ to FASTA |FASTQ | | |★★ |
| |[fa2fq](https://bioinf.shenwei.me/seqkit/usage/#fa2fq) |retrieve corresponding FASTQ records by a FASTA file |FASTA/Q | | | |
| |[fx2tab](https://bioinf.shenwei.me/seqkit/usage/#fx2tab-tab2fx) |convert FASTA/Q to tabular format |FASTA/Q | | |★★ |
| |[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#fx2tab-tab2fx) |convert tabular format to FASTA/Q format |FASTA/Q | | | |
| |[convert](https://bioinf.shenwei.me/seqkit/usage/#convert) |convert FASTQ quality encoding between Sanger, Solexa and Illumina |FASTA/Q | | | |
| |[translate](https://bioinf.shenwei.me/seqkit/usage/#translate) |translate DNA/RNA to protein sequence |FASTA/Q |+ or/and - | |★★ |
|searching |[grep](https://bioinf.shenwei.me/seqkit/usage/#grep) |search sequences by ID/name/sequence/sequence motifs, mismatch allowed |FASTA/Q |+ and - |partly, -m |★★★★★ |
| |[locate](https://bioinf.shenwei.me/seqkit/usage/#locate) |locate subsequences/motifs, mismatch allowed |FASTA/Q |+ and - |partly, -m |★★★★★ |
| |[amplicon](https://bioinf.shenwei.me/seqkit/usage/#amplicon) |extract amplicon (or specific region around it), mismatch allowed |FASTA/Q |+ and - |partly, -m |★ |
| |[fish](https://bioinf.shenwei.me/seqkit/usage/#fish) |look for short sequences in larger sequences |FASTA/Q |+ and - | | |
|set operation |[sample](https://bioinf.shenwei.me/seqkit/usage/#sample) |sample sequences by number or proportion |FASTA/Q | | |★★★★ |
| |[rmdup](https://bioinf.shenwei.me/seqkit/usage/#rmdup) |remove duplicated sequences by ID/name/sequence |FASTA/Q |+ and - | |★★★ |
| |[common](https://bioinf.shenwei.me/seqkit/usage/#common) |find common sequences of multiple files by id/name/sequence |FASTA/Q |+ and - | | |
| |[duplicate](https://bioinf.shenwei.me/seqkit/usage/#duplicate) |duplicate sequences N times |FASTA/Q | | |★ |
| |[split](https://bioinf.shenwei.me/seqkit/usage/#split) |split sequences into files by id/seq region/size/parts (mainly for FASTA) |FASTA preffered| | |★ |
| |[split2](https://bioinf.shenwei.me/seqkit/usage/#split2) |split sequences into files by size/parts (FASTA, PE/SE FASTQ) |FASTA/Q | | |★★ |
| |[head](https://bioinf.shenwei.me/seqkit/usage/#head) |print first N FASTA/Q records |FASTA/Q | | | |
| |[head-genome](https://bioinf.shenwei.me/seqkit/usage/#head-genome) |print sequences of the first genome with common prefixes in name |FASTA/Q | | | |
| |[range](https://bioinf.shenwei.me/seqkit/usage/#range) |print FASTA/Q records in a range (start:end) |FASTA/Q | | | |
| |[pair](https://bioinf.shenwei.me/seqkit/usage/#pair) |match up paired-end reads from two fastq files |FASTA/Q | | | |
|edit |[concat](https://bioinf.shenwei.me/seqkit/usage/#concat) |concatenate sequences with same the ID from multiple files |FASTA/Q |+ only | |★★★ |
| |[replace](https://bioinf.shenwei.me/seqkit/usage/#replace) |replace name/sequence by regular expression |FASTA/Q |+ only | |★★ |
| |[restart](https://bioinf.shenwei.me/seqkit/usage/#restart) |reset start position for circular genome |FASTA/Q |+ only | |★ |
| |[mutate](https://bioinf.shenwei.me/seqkit/usage/#mutate) |edit sequence (point mutation, insertion, deletion) |FASTA/Q |+ only | | |
| |[rename](https://bioinf.shenwei.me/seqkit/usage/#rename) |rename duplicated IDs |FASTA/Q | | |★ |
|ordering |[sort](https://bioinf.shenwei.me/seqkit/usage/#sort) |sort sequences by id/name/sequence/length |FASTA preffered| | |★★ |
| |[shuffle](https://bioinf.shenwei.me/seqkit/usage/#shuffle) |shuffle sequences |FASTA preffered| | | |
|BAM processing |[bam](https://bioinf.shenwei.me/seqkit/usage/#bam) |monitoring and online histograms of BAM record features |BAM | | | |
Notes:
- Strand-sensitivity:
- `+ only`: only processing on the positive/forward strand.
- `+ and -`: searching on both strands.
- `+ or/and -`: depends on users' flags/options/arguments.
- Multiple-threads: Using the default 4 threads is fast enough for most commands, some commands can benefit from extra threads.
- Popularity: Bases on statistics of 227 publications citing seqkit since 2020.
## Citation
**W Shen**, S Le, Y Li\*, F Hu\*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
***PLOS ONE***. [doi:10.1371/journal.pone.0163962](https://doi.org/10.1371/journal.pone.0163962).
## Contributors
- [Wei Shen](https://github.com/shenwei356)
- [Botond Sipos](https://github.com/bsipos): `bam`, `scat`, `fish`, `sana`, `watch`.
- [others](https://github.com/shenwei356/seqkit/graphs/contributors)
## Acknowledgements
We thank [Lei Zhang](https://github.com/jameslz) for testing SeqKit,
and also thank [Jim Hester](https://github.com/jimhester/),
author of [fasta_utilities](https://github.com/jimhester/fasta_utilities),
for advice on early performance improvements of for FASTA parsing
and [Brian Bushnell](https://twitter.com/BBToolsBio),
author of [BBMaps](https://sourceforge.net/projects/bbmap/),
for advice on naming SeqKit and adding accuracy evaluation in benchmarks.
We also thank Nicholas C. Wu from the Scripps Research Institute,
USA for commenting on the manuscript
and [Guangchuang Yu](http://guangchuangyu.github.io/)
from State Key Laboratory of Emerging Infectious Diseases,
The University of Hong Kong, HK for advice on the manuscript.
We thank [Li Peng](https://github.com/penglbio) for reporting many bugs.
We appreciate [Klaus Post](https://github.com/klauspost) for his fantastic packages (
[compress](https://github.com/klauspost/compress) and [pgzip](https://github.com/klauspost/pgzip)
) which accelerate gzip file reading and writing.
## Contact
[Create an issue](https://github.com/shenwei356/seqkit/issues) to report bugs,
propose new functions or ask for help.
## License
[MIT License](https://github.com/shenwei356/seqkit/blob/master/LICENSE)
## Starchart
