domain-bioinformatics

bedtools - the swiss army knife for genome arithmetic

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Foundation Models for Genomics & Transcriptomics

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.

Official code repository for GATK versions 4 and up

Single-cell analysis in Python. Scales to >100M cells.

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Annotated data.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

IQ-TREE software version 2: phylogenetics by maximum likelihood

C library for high-throughput sequencing data formats

A comprehensive library for computational molecular biology

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

Tools (written in C using htslib) for manipulating next-generation sequencing data

Oxford Nanopore's Basecaller

The second version of the Kraken taxonomic sequence classification system

Official git repository for Biopython (originally converted from CVS)

Prediction of binding residues for metal ions, nucleic acids, and small molecules.