# shenwei356/seqkit

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

Repository: https://github.com/shenwei356/seqkit
Canonical: https://ross.abutalabs.com/products/seqkit
Homepage: https://bioinf.shenwei.me/seqkit
Language: Go
License: MIT
License Family: permissive
Topics: bioinformatics, cross-platform, fasta, golang, sequence, toolkit, fastq, tool, manipulation
Last push: 2026-08-21T15:30:37+00:00

## Health v2 (maintenance only)
Score: 81/100 (v2, computed 2026-09-02T17:46:02.011165+00:00)
- activity 98, release rhythm 48, longevity 100
- inputs: {"age_days": 3839, "days_push": 12, "days_rel": 187, "gap_med": 93, "n_releases_24m": 6}
- flags: none
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1590, forks 185 (observed 2026-08-28T04:05:08.473838+00:00)

## What it is
SeqKit is an ultrafast, cross-platform command-line toolkit written in Go for manipulating FASTA and FASTQ sequence files, offering 38+ subcommands for tasks like statistics, subsequence extraction, filtering, translation, and deduplication. It ships as dependency-free static binaries, supports compressed input/output and Unix pipes, and is installable via conda, homebrew, or direct download.

## Use cases
- compute statistics like sequence count, N50, and GC content for FASTA/FASTQ files
- extract subsequences from FASTA files by region, BED, or GTF coordinates
- filter FASTQ reads by length or quality
- remove duplicate sequence records from FASTA/FASTQ files
- translate DNA/RNA sequences to protein
- split or sort large FASTA files by header or length
- extract paired-end reads from two FASTQ files
- search for motifs or enzyme restriction sites in sequences

## When to choose
- you need fast, dependency-free manipulation of FASTA/FASTQ files on any platform
- you want to script sequence file processing in Unix pipelines with gzip/xz/zstd/bzip2/lz4 support
- you need reproducible sampling or shuffling of large sequence datasets
- you want a single tool covering common sequence manipulations instead of ad-hoc awk/sed scripts

## When to avoid
- you need alignment, assembly, or variant calling rather than sequence file manipulation
- you require a programmatic library API rather than a command-line tool
- your workflow depends on format-specific tools like samtools for indexed BAM processing

## Facets
- artifact type: cli-tool
- maturity: active
- function: cli, parser, developer-tools
- domain: bioinformatics, files
- platform: windows, cross-platform, cli
- tags: fasta, fastq, sequence-analysis, genomics, golang, bioconda, sequence-manipulation, ngs, command-line, linux, macos

## Member repositories
- shenwei356/seqkit (main) score 81

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:05:08.473838+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T03:54:48.262779+00:00, confidence not recorded.
  - readme: https://github.com/shenwei356/seqkit (fetched 2026-08-28T04:05:08.473838+00:00, sha 42db4dd794df)
  - homepage: https://bioinf.shenwei.me/seqkit (fetched 2026-08-29T11:25:26.830216+00:00, sha 6fe993f11541)
  - site_page: https://bioinf.shenwei.me/seqkit/faq (fetched 2026-08-29T11:25:26.839653+00:00, sha 42a551b37111)
  - site_page: http://bioinf.shenwei.me/seqkit/faq (fetched 2026-08-29T11:25:26.841571+00:00, sha 42a551b37111)
- Data as of 2026-08-30T08:39:29.467469+00:00.