FASTA/FASTQ pre-processing programs
☆202Mar 4, 2022Updated 4 years ago
Alternatives and similar repositories for fastx_toolkit
Users that are interested in fastx_toolkit are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Gordon's Text utils Library☆10Apr 11, 2022Updated 4 years ago
- Fast genome analysis from unassembled short reads☆320Apr 8, 2024Updated 2 years ago
- Program for aligning DNA sequences, a pairwise aligner.☆245Mar 27, 2026Updated last month
- Next generation sequencing reads de novo assembler.☆240Sep 20, 2025Updated 7 months ago
- Transcript assembly and quantification for RNA-Seq☆508Dec 26, 2025Updated 4 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Assemble large genomes using short reads☆328Updated this week
- Cutadapt removes adapter sequences from sequencing reads☆578Apr 6, 2026Updated 3 weeks ago
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,061Apr 25, 2026Updated last week
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆240Aug 11, 2021Updated 4 years ago
- Trinity RNA-Seq de novo transcriptome assembly☆891Apr 23, 2026Updated last week
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆272Mar 15, 2026Updated last month
- BEDOPS: high-performance genomic feature operations☆368Apr 29, 2025Updated last year
- Spliced read mapper for RNA-Seq☆92Jul 9, 2023Updated 2 years ago
- A fast multi-threaded k-mer counter☆538Mar 20, 2024Updated 2 years ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- An ultrafast memory-efficient short read aligner☆267May 11, 2022Updated 3 years ago
- De novo construction of isoforms from long-read data☆35Jun 10, 2025Updated 10 months ago
- De novo clustering of long transcript reads into genes☆76Apr 27, 2025Updated last year
- ☆97Sep 21, 2022Updated 3 years ago
- Simple FASTQ quality assessment using Python☆109Feb 24, 2026Updated 2 months ago
- Pan-genome wide association studies☆215May 29, 2024Updated last year
- bedtools - the swiss army knife for genome arithmetic☆1,030Mar 11, 2025Updated last year
- Pilon is an automated genome assembly improvement and variant detection tool☆380Apr 10, 2022Updated 4 years ago
- MUMmer for HPC☆18Jan 7, 2013Updated 13 years ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Graph-based alignment (Hierarchical Graph FM index)☆534Jan 27, 2026Updated 3 months ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆239Dec 29, 2023Updated 2 years ago
- Ultra-fast de novo assembler using long noisy reads☆136Feb 24, 2021Updated 5 years ago
- Fast and accurately polish the genome generated by long reads.☆243Jan 9, 2025Updated last year
- ☆348Mar 4, 2025Updated last year
- The final version 2 release of our software to detect core genes in eukaryotic genomes☆30Mar 31, 2015Updated 11 years ago
- emapper-utils: utils for parse emapper result☆10Sep 22, 2020Updated 5 years ago
- Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo sh…☆298Oct 13, 2025Updated 6 months ago
- Windowed Adaptive Trimming for fastq files using quality☆228May 8, 2017Updated 8 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆477Apr 10, 2026Updated 3 weeks ago
- Toolkit for processing sequences in FASTA/Q formats☆1,538Jun 1, 2025Updated 11 months ago
- Ultrafast de novo assembly for long noisy reads (though having no consensus step)☆353Jul 19, 2025Updated 9 months ago
- UCSC command line bioinformatic utilities☆189Jul 31, 2024Updated last year
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,731Mar 22, 2025Updated last year
- A fast lossless FASTQ compressor with ultra-high compression ratio☆148May 28, 2025Updated 11 months ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆401Aug 30, 2025Updated 8 months ago