bedtools - the swiss army knife for genome arithmetic
A versatile pairwise aligner for genomic and spliced nucleotide sequences
The second version of the Kraken taxonomic sequence classification system
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
C library for high-throughput sequencing data formats
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Foundation Models for Genomics & Transcriptomics
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
Official code repository for GATK versions 4 and up
Oxford Nanopore's Basecaller
Tools (written in C using htslib) for manipulating next-generation sequencing data
To associate your repository with the domain-genomics topic, visit your repo's landing page and select "manage topics."