SeqKit is a fast, cross-platform command-line toolkit for manipulating FASTA and FASTQ files. It offers commands for inspecting, filtering, searching, converting and editing biological sequences.
This is free and open source software.
Key Features
- Reads FASTA and FASTQ files seamlessly.
- Processes gzip, xz, zstd, bzip2 and lz4 compressed data.
- Supports files, standard input and standard output.
- Calculates statistics including N50, Q20 and Q30 values.
- Filters sequences by length, quality and other properties.
- Extracts subsequences by region, GTF or BED data.
- Searches by identifiers, names, sequences and motifs.
- Allows mismatches when searching sequences.
- Converts between FASTA, FASTQ and tabular formats.
- Samples, deduplicates, splits, sorts and shuffles sequences.
- Supports sequence replacement, mutation, insertion and deletion.
- Translates DNA and RNA sequences into proteins.
- Handles paired-end reads and circular genomes.
- Generates online histograms of sequence properties.
- Offers multithreading for supported operations.
- Provides Bash and Zsh command completion.
Website: github.com/shenwei356/seqkit
Support:
Developer: Wei Shen
License: MIT License
SeqKit is written in Go. Learn Go with our recommended free books and free tutorials.
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Read our verdict in the software roundup.
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