An ultrafast memory-efficient short read aligner
☆267May 11, 2022Updated 4 years ago
Alternatives and similar repositories for bowtie
Users that are interested in bowtie are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A fast and sensitive gapped read aligner☆804Jun 1, 2026Updated last month
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,759Updated this week
- Graph-based alignment (Hierarchical Graph FM index)☆540Jan 27, 2026Updated 6 months ago
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,932Updated this week
- Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities☆25Oct 31, 2019Updated 6 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Minimalistic aligner which uses Minimap for input mapping locations and Edlib for fast bitvector alignment.☆10Jul 16, 2017Updated 9 years ago
- bedtools - the swiss army knife for genome arithmetic☆1,042Jun 10, 2026Updated last month
- FASTA/FASTQ pre-processing programs☆202Mar 4, 2022Updated 4 years 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
- BEDOPS: high-performance genomic feature operations☆374Apr 29, 2025Updated last year
- ☆323Mar 31, 2020Updated 6 years ago
- Spliced read mapper for RNA-Seq☆92Jul 9, 2023Updated 3 years ago
- Cutadapt removes adapter sequences from sequencing reads☆586Updated this week
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆472Updated this week
- 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.
- C library for high-throughput sequencing data formats☆939Updated this week
- Tools for working with SAM/BAM data☆613Dec 22, 2024Updated last year
- flexible barcode and adapter removal☆81Feb 10, 2023Updated 3 years ago
- Official code repository for GATK versions 4 and up☆1,978Updated this week
- Long Approximate Matches-based Split Aligner☆13Apr 6, 2017Updated 9 years ago
- Tools for bam file processing☆56Apr 20, 2015Updated 11 years ago
- A fast multi-threaded k-mer counter☆547Mar 20, 2024Updated 2 years ago
- RNA-seq aligner☆2,229Mar 18, 2025Updated last year
- Near-optimal RNA-Seq quantification☆767Jul 12, 2026Updated 2 weeks 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.
- Tools to process and analyze deep sequencing data.☆762Updated this week
- Ultrafast de novo assembly for long noisy reads (though having no consensus step)☆356Jul 19, 2025Updated last year
- Trinity RNA-Seq de novo transcriptome assembly☆896Apr 23, 2026Updated 3 months ago
- RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.☆14Nov 10, 2025Updated 8 months ago
- Fast and memory-efficient sequencing error corrector☆96Jan 4, 2026Updated 6 months ago
- Tools for early stage alignment file processing☆96Mar 12, 2019Updated 7 years ago
- de novo sequence assembler using string graphs☆244Aug 8, 2019Updated 6 years ago
- Reads simulator☆285Sep 3, 2021Updated 4 years ago
- CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA targets☆21Mar 28, 2021Updated 5 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- BWK awk modified for biological data☆641Aug 11, 2022Updated 3 years ago
- To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be co…☆31Dec 26, 2023Updated 2 years ago
- C++ API & command-line toolkit for working with BAM data☆432May 18, 2025Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,221May 19, 2026Updated 2 months ago
- Toolkit for processing sequences in FASTA/Q formats☆1,550Jun 1, 2025Updated last year
- Integrated Variant Caller☆17Mar 15, 2018Updated 8 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