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☆324Apr 8, 2024Updated 2 years ago
- Program for aligning DNA sequences, a pairwise aligner.☆251May 20, 2026Updated 2 months ago
- Next generation sequencing reads de novo assembler.☆240Sep 20, 2025Updated 10 months ago
- Transcript assembly and quantification for RNA-Seq☆525Jun 3, 2026Updated last month
- 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☆331Apr 30, 2026Updated 2 months ago
- Cutadapt removes adapter sequences from sequencing reads☆586Jun 26, 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.☆1,069Jun 13, 2026Updated last month
- Trinity RNA-Seq de novo transcriptome assembly☆896Apr 23, 2026Updated 3 months ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆243Aug 11, 2021Updated 4 years ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆276Jul 7, 2026Updated 2 weeks ago
- A fast multi-threaded k-mer counter☆547Mar 20, 2024Updated 2 years ago
- BEDOPS: high-performance genomic feature operations☆374Apr 29, 2025Updated last year
- An ultrafast memory-efficient short read aligner☆267May 11, 2022Updated 4 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.
- Simple FASTQ quality assessment using Python☆109Feb 24, 2026Updated 5 months ago
- De novo clustering of long transcript reads into genes☆80Apr 27, 2025Updated last year
- Pan-genome wide association studies☆219May 29, 2024Updated 2 years ago
- bedtools - the swiss army knife for genome arithmetic☆1,042Jun 10, 2026Updated last month
- Graph-based alignment (Hierarchical Graph FM index)☆540Jan 27, 2026Updated 5 months ago
- ☆97Sep 21, 2022Updated 3 years ago
- Ultra-fast de novo assembler using long noisy reads☆137Feb 24, 2021Updated 5 years ago
- Pilon is an automated genome assembly improvement and variant detection tool☆383Apr 10, 2022Updated 4 years ago
- Fast and accurately polish the genome generated by long reads.☆243Jan 9, 2025Updated last year
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- De novo construction of isoforms from long-read data☆38Jul 2, 2026Updated 3 weeks ago
- ☆350Mar 4, 2025Updated last year
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆241Dec 29, 2023Updated 2 years ago
- Windowed Adaptive Trimming for fastq files using quality☆229May 8, 2017Updated 9 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…☆297Oct 13, 2025Updated 9 months ago
- The final version 2 release of our software to detect core genes in eukaryotic genomes☆30Mar 31, 2015Updated 11 years ago
- Ultrafast de novo assembly for long noisy reads (though having no consensus step)☆356Jul 19, 2025Updated last year
- Toolkit for processing sequences in FASTA/Q formats☆1,549Jun 1, 2025Updated last year
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆490Jul 7, 2026Updated 2 weeks ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Pipeline for the identification of (coding) gene structures in draft genomes.☆38May 9, 2024Updated 2 years ago
- emapper-utils: utils for parse emapper result☆10Sep 22, 2020Updated 5 years ago
- UCSC command line bioinformatic utilities☆190Jul 31, 2024Updated last year
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,758Jun 20, 2026Updated last month
- SRA Tools☆1,357Updated this week
- A fast and sensitive gapped read aligner☆803Jun 1, 2026Updated last month
- A fast lossless FASTQ compressor with ultra-high compression ratio☆152May 28, 2025Updated last year