Foundation Models for Genomics & Transcriptomics

bedtools - the swiss army knife for genome arithmetic

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.

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

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

Official git repository for Biopython (originally converted from CVS)

The second version of the Kraken taxonomic sequence classification system

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

A comprehensive library for computational molecular biology

Official code repository for GATK versions 4 and up

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

C library for high-throughput sequencing data formats

IQ-TREE software version 2: phylogenetics by maximum likelihood

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

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

Oxford Nanopore's Basecaller

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

A versatile pairwise aligner for genomic and spliced nucleotide sequences