BenLangmead / bowtie2View external linksLinks
A fast and sensitive gapped read aligner
☆771Updated this week
Alternatives and similar repositories for bowtie2
Users that are interested in bowtie2 are comparing it to the libraries listed below
Sorting:
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,701Mar 22, 2025Updated 10 months ago
- An ultrafast memory-efficient short read aligner☆266May 11, 2022Updated 3 years ago
- Graph-based alignment (Hierarchical Graph FM index)☆528Jan 27, 2026Updated 2 weeks ago
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,839Updated this week
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,126Dec 12, 2025Updated 2 months ago
- bedtools - the swiss army knife for genome arithmetic☆1,022Mar 11, 2025Updated 11 months ago
- A quality control analysis tool for high throughput sequencing data☆580Jan 5, 2026Updated last month
- SPAdes Genome Assembler☆905Feb 2, 2026Updated last week
- Cutadapt removes adapter sequences from sequencing reads☆570Jan 12, 2026Updated last month
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,283Jan 22, 2026Updated 3 weeks ago
- The next version of bwa-mem☆816Oct 15, 2025Updated 4 months ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,419Jan 15, 2026Updated last month
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,049Feb 4, 2026Updated last week
- Toolkit for processing sequences in FASTA/Q formats☆1,526Jun 1, 2025Updated 8 months ago
- Official code repository for GATK versions 4 and up☆1,907Feb 8, 2026Updated last week
- RNA-seq aligner☆2,136Mar 18, 2025Updated 10 months ago
- Accelerated BLAST compatible local sequence aligner.☆1,239Feb 7, 2026Updated last week
- Assemble large genomes using short reads☆327Mar 27, 2025Updated 10 months ago
- A fast multi-threaded k-mer counter☆529Mar 20, 2024Updated last year
- Mummer alignment tool☆548Feb 4, 2025Updated last year
- The second version of the Kraken taxonomic sequence classification system☆868Jan 30, 2026Updated 2 weeks ago
- Trinity RNA-Seq de novo transcriptome assembly☆882Feb 7, 2025Updated last year
- Transcript assembly and quantification for RNA-Seq☆487Dec 26, 2025Updated last month
- Program for aligning DNA sequences, a pairwise aligner.☆239Jun 16, 2025Updated 7 months ago
- Ultra-fast and memory-efficient (meta-)genome assembler☆693Oct 28, 2025Updated 3 months ago
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,509Updated this week
- Automatically exported from code.google.com/p/cdhit☆718Oct 11, 2022Updated 3 years ago
- A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…☆539Jan 22, 2026Updated 3 weeks ago
- SRA Tools☆1,300Feb 6, 2026Updated last week
- De novo assembler for single molecule sequencing reads using repeat graphs☆903May 2, 2025Updated 9 months ago
- Tools for working with SAM/BAM data☆605Dec 22, 2024Updated last year
- ☆286Oct 15, 2025Updated 4 months ago
- Fast genome-wide functional annotation through orthology assignment☆700Jun 18, 2025Updated 7 months ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆717Updated this week
- A single molecule sequence assembler for genomes large and small.☆693Nov 13, 2025Updated 3 months ago
- Next generation sequencing reads de novo assembler.☆239Sep 20, 2025Updated 4 months ago
- Genome assembly evaluation tool☆494Nov 14, 2024Updated last year
- C library for high-throughput sequencing data formats☆906Feb 6, 2026Updated last week
- Read trimming tool for Illumina NGS data.☆149Mar 10, 2015Updated 10 years ago