shenwei356/seqkit

Health v2 · maintenance only

Adoption not part of the score

1590 stars · 185 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

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

cli-tool · maturity active

cli parser developer-tools bioinformatics files windows cross-platform cli fasta fastq sequence-analysis genomics golang bioconda sequence-manipulation ngs command-line linux macos

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markdown · JSON · MCP: product_card(name="shenwei356/seqkit")