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# 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)
[![GitHub stars](https://img.shields.io/github/stars/shenwei356/seqkit.svg?style=social&label=Star&?maxAge=2592000)](https://github.com/shenwei356/seqkit)
[![license](https://img.shields.io/github/license/shenwei356/seqkit.svg?maxAge=2592000)](https://github.com/shenwei356/seqkit/blob/master/LICENSE)
- **Latest version:** [![Latest Version](https://img.shields.io/github/release/shenwei356/seqkit.svg?style=flat?maxAge=86400)](https://github.com/shenwei356/seqkit/releases)
[![Github Releases](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/total.svg?maxAge=3600)](http://bioinf.shenwei.me/seqkit/download/)
[![Cross-platform](https://img.shields.io/badge/platform-any-ec2eb4.svg?style=flat)](http://bioinf.shenwei.me/seqkit/download/)
[![Anaconda Cloud](https://anaconda.org/bioconda/seqkit/badges/version.svg)](https://anaconda.org/bioconda/seqkit)
- **[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)
[![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)
- **Others**: [![check in Biotreasury](https://img.shields.io/badge/Biotreasury-collected-brightgreen)](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
- `conda install -c bioconda seqkit`
- **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`/`bzip2` 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 autocompletion](http://bioinf.shenwei.me/seqkit/download/#shell-completion)
- **Versatile commands** ([usages and examples](http://bioinf.shenwei.me/seqkit/usage/))
- Practical functions supported by [38 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|
|:----------------|:-------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------|:-----------------|:------------|
|Basic operation |[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 | |✓ |
| |[subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq) |Get subsequences by region/gtf/bed, including flanking sequences |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 the FASTA index file and extract subsequences (with more features than samtools faidx)|FASTA |+ or/and - | |
| |[translate](https://bioinf.shenwei.me/seqkit/usage/#translate) |translate DNA/RNA to protein sequence |FASTA/Q |+ or/and - | |
| |[watch ](https://bioinf.shenwei.me/seqkit/usage/#watch ) |Monitoring and online histograms of sequence features |FASTA/Q | | |
| |[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 format |FASTQ | | |
| |[fx2tab](https://bioinf.shenwei.me/seqkit/usage/#fx2tab) |Convert FASTA/Q to tabular format |FASTA/Q | | |
| |[fa2fq](https://bioinf.shenwei.me/seqkit/usage/#fa2fq) |Retrieve corresponding FASTQ records by a FASTA file |FASTA/Q |+ only | |
| |[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#tab2fx) |Convert tabular format to FASTA/Q format |TSV | | |
| |[convert](https://bioinf.shenwei.me/seqkit/usage/#convert) |Convert FASTQ quality encoding between Sanger, Solexa and Illumina |FASTA/Q | | |
|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) |Patch up paired-end reads from two fastq files |FASTA/Q | | |
|Edit |[replace](https://bioinf.shenwei.me/seqkit/usage/#replace) |Replace name/sequence by regular expression |FASTA/Q |+ only | |
| |[rename](https://bioinf.shenwei.me/seqkit/usage/#rename) |Rename duplicated IDs |FASTA/Q | | |
| |[concat](https://bioinf.shenwei.me/seqkit/usage/#concat) |Concatenate sequences with same ID from multiple files |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 | |
| |[sana](https://bioinf.shenwei.me/seqkit/usage/#sana) |Sanitize broken single line FASTQ files |FASTQ | | |
|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 | | |
|Miscellaneous |[sum](https://bioinf.shenwei.me/seqkit/usage/#sum) |Compute message digest for all sequences in FASTA/Q files |FASTA/Q | |✓ |
| |[merge-slides](https://bioinf.shenwei.me/seqkit/usage/#merge-slides)|Merge sliding windows generated from seqkit sliding |TSV | |

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.

## 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).
<span class="__dimensions_badge_embed__" data-doi="10.1371/journal.pone.0163962" data-style="small_rectangle"></span>

## Contributors

- [Wei Shen](https://github.com/shenwei356)
- [Botond Sipos](https://github.com/botond-sipos): `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

<img src="https://starchart.cc/shenwei356/seqkit.svg" alt="Stargazers over time" style="max-width: 100%">

28 changes: 14 additions & 14 deletions doc/docs/usage.md
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Expand Up @@ -468,7 +468,7 @@ Usage
``` text
get subsequences by region/gtf/bed, including flanking sequences.
Attentions:
Attention:
1. Use "seqkit grep" for extract subsets of sequences.
"seqtk subseq seqs.fasta id.txt" equals to
"seqkit grep -f id.txt seqs.fasta"
Expand Down Expand Up @@ -696,7 +696,7 @@ Columns:
17. AvgQual average quality
18. GC(%) percentage of GC content
Attentions:
Attention:
1. Sequence length metrics (sum_len, min_len, avg_len, max_len, Q1, Q2, Q3)
count the number of gaps or spaces. You can remove them with "seqkit seq -g":
seqkit seq -g input.fasta | seqkit stats
Expand Down Expand Up @@ -826,7 +826,7 @@ Usage
```text
compute message digest for all sequences in FASTA/Q files
Attentions:
Attention:
1. Sequence headers and qualities are skipped, only sequences matter.
2. The order of sequences records does not matter.
3. Circular complete genomes are supported with the flag -c/--circular.
Expand Down Expand Up @@ -955,7 +955,7 @@ This command is similar with "samtools faidx" but has some extra features:
3. if you have large number of IDs, you can use:
seqkit faidx seqs.fasta -l IDs.txt
Attentions:
Attention:
1. The flag -U/--update-faidx is recommended to ensure the .fai file matches the FASTA file.
The definition of region is 1-based and with some custom design.
Expand Down Expand Up @@ -1636,7 +1636,7 @@ Usage
``` text
search sequences by ID/name/sequence/sequence motifs, mismatch allowed
Attentions:
Attention:
0. By default, we match sequence ID with patterns, use "-n/--by-name"
for matching full name instead of just ID.
Expand Down Expand Up @@ -1824,7 +1824,7 @@ Usage
``` text
locate subsequences/motifs, mismatch allowed
Attentions:
Attention:
1. Motifs could be EITHER plain sequence containing "ACTGN" OR regular
expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.
Expand Down Expand Up @@ -2056,7 +2056,7 @@ Usage
``` text
extract amplicon (or specific region around it) via primer(s).
Attentions:
Attention:
1. Only one (the longest) matching location is returned for every primer pair.
2. Mismatch is allowed, but the mismatch location (5' or 3') is not controled.
You can increase the value of "-j/--threads" to accelerate processing.
Expand Down Expand Up @@ -2305,7 +2305,7 @@ Usage
``` text
remove duplicated sequences by ID/name/sequence
Attentions:
Attention:
1. When comparing by sequences, both positive and negative strands are
compared. Switch on -P/--only-positive-strand for considering the
positive strand only.
Expand Down Expand Up @@ -2530,7 +2530,7 @@ If you want to cut a sequence into multiple segments.
E.g., cutting into segments of 40 bp and keeping the last segment which can be shorter than 40 bp.
seqkit sliding -g -s 40 -W 40 input.fasta -o out.fasta
Attentions:
Attention:
1. For the two-pass mode (-2/--two-pass), The flag -U/--update-faidx is recommended to
ensure the .fai file matches the FASTA file.
Expand Down Expand Up @@ -2791,7 +2791,7 @@ Usage
```text
match up paired-end reads from two fastq files
Attentions:
Attention:
1. Orders of headers in the two files better be the same (not shuffled),
otherwise, it consumes a huge number of memory for buffering reads in memory.
2. Unpaired reads are optional outputted with the flag -u/--save-unpaired.
Expand Down Expand Up @@ -3418,7 +3418,7 @@ Usage
``` text
concatenate sequences with same ID from multiple files
Attentions:
Attention:
1. By default, only sequences with IDs that appear in all files are outputted.
use -f/--full to output all sequences.
2. If there are more than one sequences of the same ID, we output the Cartesian
Expand Down Expand Up @@ -3481,7 +3481,7 @@ Usage
``` text
edit sequence (point mutation, insertion, deletion)
Attentions:
Attention:
1. Mutiple point mutations (-p/--point) are allowed, but only single
insertion (-i/--insertion) OR single deletion (-d/--deletion) is allowed.
Expand Down Expand Up @@ -3694,7 +3694,7 @@ seqkit will write the sequences to temporary files, and create FASTA index.
Secondly, seqkit shuffles sequence IDs and extract sequences by FASTA index.
Attentions:
Attention:
1. For the two-pass mode (-2/--two-pass), The flag -U/--update-faidx is recommended to
ensure the .fai file matches the FASTA file.
Expand Down Expand Up @@ -3757,7 +3757,7 @@ seqkit will write the sequences to temporary files, and create FASTA index.
Secondly, seqkit sorts sequence by head and length information
and extracts sequences by FASTA index.
Attentions:
Attention:
1. For the two-pass mode (-2/--two-pass), The flag -U/--update-faidx is recommended to
ensure the .fai file matches the FASTA file.
Expand Down
2 changes: 1 addition & 1 deletion seqkit/cmd/amplicon.go
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Expand Up @@ -52,7 +52,7 @@ var ampliconCmd = &cobra.Command{
Short: "extract amplicon (or specific region around it) via primer(s)",
Long: `extract amplicon (or specific region around it) via primer(s).
Attentions:
Attention:
1. Only one (the longest) matching location is returned for every primer pair.
2. Mismatch is allowed, but the mismatch location (5' or 3') is not controlled.
You can increase the value of "-j/--threads" to accelerate processing.
Expand Down
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