Foundation Models for Genomics & Transcriptomics
bedtools - the swiss army knife for genome arithmetic
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.
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.
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
A comprehensive library for computational molecular biology
Official git repository for Biopython (originally converted from CVS)
The second version of the Kraken taxonomic sequence classification system
Oxford Nanopore's Basecaller
Tools (written in C using htslib) for manipulating next-generation sequencing data
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.
C library for high-throughput sequencing data formats
Official code repository for GATK versions 4 and up
Single-cell analysis in Python. Scales to >100M cells.
A versatile pairwise aligner for genomic and spliced nucleotide sequences
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
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