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.
Related Software
| Bioinformatics Tools | |
|---|---|
| Bioconductor | Analysis and comprehension of high-throughput genomic data |
| Biopython | Tools for biological computation written in Python |
| UGENE | Set of integrated bioinformatics software |
| BioPerl | Perl tools for computational molecular biology |
| GROMACS | Versatile package to perform molecular dynamics |
| IGV | High-performance visualization genome browser tool |
| GATK | Genomic analysis toolkit focused on variant discovery |
| BioJava | Provides Java tools for processing biological data |
| InterMine | Integrate biological data sources |
| bedtools | Powerful toolset for genome arithmetic |
| EMBOSS | The European Molecular Biology Open Software Suite |
| BLAST | Algorithm for comparing primary biological sequence information |
| Galaxy | Web-based platform for data-intensive computational research |
| minimap2 | Versatile sequence alignment program |
| Scanpy | Scalable analysis of single-cell gene expression data |
| Jalview | Multiple sequence alignment editing, visualisation and analysis |
| SeqKit | Fast toolkit for manipulating FASTA and FASTQ sequence files |
| samtools | Manipulate next-generation sequencing data |
| MultiQC | Aggregates results from multiple bioinformatics analyses |
| BCFtools | Variant calling and manipulating files in the Variant Call Format |
| Foldseek | Fast searching and comparison of large protein structure datasets |
| FastQC | Quality control tool for high throughput sequence data |
| SPAdes | Versatile toolkit for assembling and analysing sequencing data |
| GenomeTools | Collection of bioinformatics tools |
| AliView | Alignment viewer and editor |
| mothur | Analyze microbial communities |
| Bandage | Visualising de novo assembly graphs |
| cramino | BAM/CRAM quality evaluation |
| abPOA | Adaptive banded Partial Order Alignment |
Read our verdict in the software roundup.
 Explore our carefully curated directory of recommended free and open source software, covering every major software category.The directory forms part of our extensive collection of articles for Linux enthusiasts. It includes hundreds of detailed reviews, together with free and open source alternatives to proprietary software from companies such as Google, Microsoft, Apple, Adobe, IBM, Cisco, Oracle, and Autodesk. LinuxLinks also covers interesting projects worth exploring, Linux-compatible hardware, free programming books and tutorials, and much more. Know a useful free and open source Linux application that we haven’t covered? Tell us about it using our submission form. |
Please read our Comment Policy before commenting.