lh3/seqtk

Health v2 · maintenance only

Adoption not part of the score

1559 stars · 325 forks observed · 2026-08-28

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

Seqtk is a fast, lightweight C command-line toolkit for processing sequences in FASTA and FASTQ formats, with optional gzip support and only zlib as a dependency. It supports format conversion, quality filtering, reverse complementing, subsetting, trimming, and repeat detection.

Use cases

• convert fastq to fasta
• reverse complement sequences in a fasta file
• subsample reads from large paired fastq files
• trim low-quality bases from sequencing reads
• extract sequences by name or genomic region
• convert multi-line fastq to standard 4-line format
• mask low-quality bases or bed regions in sequences
• find telomere repeats in a genome assembly

When to choose

• you need quick, dependency-light manipulation of FASTA/FASTQ files
• you want to subsample or subset large sequencing datasets from the command line
• you need quality-based trimming or masking in a scriptable pipeline

When to avoid

• you need alignment, assembly, or variant calling rather than sequence file manipulation
• you prefer a GUI or interactive exploration of sequence data
• you need rich metadata handling beyond FASTA/FASTQ formats

Facets

cli-tool · maturity stable

cli parser file-system developer-tools bioinformatics files windows cli cross-platform fasta fastq sequence-processing genomics c command-line linux macos

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