rsomics-fasta-utils

A toolkit of small FASTA operations under one binary — counting, filtering, converting, and reshaping FASTA records. Covers the everyday seqkit / seqtk verbs.

Install

cargo install rsomics-fasta-utils

Usage

rsomics-fasta-utils count genome.fa
rsomics-fasta-utils revcomp genome.fa -o rc.fa
rsomics-fasta-utils filter -m 500 -M 2000 genome.fa -o filtered.fa

Subcommands: chroms, composition, count, dedup, extract, filter, gc-content, grep, head, kmers, len, rename, revcomp, sample, shuffle, sort, split, tab, to-bed, to-fastq, unique, upper, window, wrap. Run rsomics-fasta-utils <cmd> --help for each command's flags; most take a positional FASTA and write to -o (- = stdout).

Origin

Independent Rust reimplementation of common FASTA operations offered by seqkit and seqtk. count, head, and revcomp are checked against seqkit stats, seqkit head, and seqkit seq -rp respectively; the remaining subcommands are self-tested for correctness rather than byte-compared to a specific upstream, so they are compatible in operation rather than guaranteed byte-identical (in particular sample / shuffle use their own RNG and will not reproduce seqkit's exact selection for a given seed).

License: MIT OR Apache-2.0. Upstream credit: seqkit (MIT), seqtk (MIT).