---
name: "seqkit"
section: "1"
platform: "linux"
package: "seqkit"
version: "2.9.0+ds-1+b4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/seqkit"
---

# seqkit(1)

cross-platform and ultrafast toolkit for FASTA/Q file manipulation

## NAME

seqkit - cross-platform and ultrafast toolkit for FASTA/Q file manipulation

## DESCRIPTION

SeqKit **--** a cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Version: 2.1.0

Author: Wei Shen \<shenwei356@gmail.com\>

Documents  : http://bioinf.shenwei.me/seqkit Source code: https://github.com/shenwei356/seqkit Please cite: https://doi.org/10.1371/journal.pone.0163962

Seqkit utlizies the pgzip (https://github.com/klauspost/pgzip) package to read and write gzip file, and the outputted gzip file would be slighty larger than files generated by GNU gzip.

Seqkit writes gzip files very fast, much faster than the multi-threaded pigz, therefore there's no need to pipe the result to gzip/pigz.

### Usage:

-

  seqkit \[command\]

### Available Commands:

- amplicon

  extract amplicon (or specific region around it) via primer(s)

- bam

  monitoring and online histograms of BAM record features

- common

  find common sequences of multiple files by id/name/sequence

- concat

  concatenate sequences with same ID from multiple files

- convert

  convert FASTQ quality encoding between Sanger, Solexa and Illumina

- duplicate

  duplicate sequences N times

- faidx

  create FASTA index file and extract subsequence

- fish

  look for short sequences in larger sequences using local alignment

- fq2fa

  convert FASTQ to FASTA

- fx2tab

  convert FASTA/Q to tabular format (and length, GC content, average quality...)

-

  genautocomplete generate shell autocompletion script (bash\|zsh\|fish\|powershell) grep            search sequences by ID/name/sequence/sequence motifs, mismatch allowed head            print first N FASTA/Q records head-genome     print sequences of the first genome with common prefixes in name locate          locate subsequences/motifs, mismatch allowed mutate          edit sequence (point mutation, insertion, deletion) pair            match up paired-end reads from two fastq files range           print FASTA/Q records in a range (start:end) rename          rename duplicated IDs replace         replace name/sequence by regular expression restart         reset start position for circular genome rmdup           remove duplicated sequences by ID/name/sequence sample          sample sequences by number or proportion sana            sanitize broken single line FASTQ files scat            real time recursive concatenation and streaming of fastx files seq             transform sequences (extract ID, filter by length, remove gaps...) shuffle         shuffle sequences sliding         extract subsequences in sliding windows sort            sort sequences by id/name/sequence/length split           split sequences into files by id/seq region/size/parts (mainly for FASTA) split2          split sequences into files by size/parts (FASTA, PE/SE FASTQ) stats           simple statistics of FASTA/Q files subseq          get subsequences by region/gtf/bed, including flanking sequences tab2fx          convert tabular format to FASTA/Q format translate       translate DNA/RNA to protein sequence (supporting ambiguous bases) version         print version information and check for update watch           monitoring and online histograms of sequence features

### Flags:

- **--alphabet-guess-seq-length** int

  length of sequence prefix of the first FASTA record based on which seqkit guesses the sequence type (0 for whole seq) (default 10000)

- **-h**, **--help**

  help for seqkit

- **--id-ncbi**

  FASTA head is NCBI-style, e.g. \>gi\|110645304\|ref\|NC\_002516.2\| Pseud...

- **--id-regexp** string

  regular expression for parsing ID (default "^(\\\\S+)\\\\s?")

- **--infile-list** string

  file of input files list (one file per line), if given, they are appended to files from cli arguments

- **-w**, **--line-width** int

  line width when outputting FASTA format (0 for no wrap) (default 60)

- **-o**, **--out-file** string

  out file ("-" for stdout, suffix .gz for gzipped out) (default "-")

- **--quiet**

  be quiet and do not show extra information

- **-t**, **--seq-type** string

  sequence type (dna\|rna\|protein\|unlimit\|auto) (for auto, it automatically detect by the first sequence) (default "auto")

- **-j**, **--threads** int

  number of CPUs. can also set with environment variable SEQKIT\_THREADS) (default 4)

Use "seqkit \[command\] **--help**" for more information about a command.

## AUTHOR

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.