Bowtie 2
github.com/benlangmead/bowtie2An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Sourced from
- Awesome Bioinformatics — github.com/benlangmead/bowtie2
- GitHub — github.com/benlangmead/bowtie2
Related resources
Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.
Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the [Open Bioinformatics Foundation](http://open-bio.org/). Contains the very useful [Entrez](https://biopython.org/DIST/docs/api/Bio.Entrez-module.html) package for API access to the NCBI databases.
Deep learning-based variant caller
Minimap2 is an pairwise aligner for genomic and spliced nucleotide sequences. It can perform the assembly-to-assembly alignment, and works with gzip'd FASTQ, FASTA formats. It also finds overlaps between long-reads.
First bioinformatics-native AI agent skill library enabling local-first, reproducible genomic and population-genetics research workflows built on OpenClaw (871+ stars, MIT License, 2026)