anndata is a Python library for storing and manipulating annotated data matrices (especially single‑cell omics) in memory and on disk, with sparse data support, lazy operations, Dask/Zarr backends and a PyTorch interface.
AUGUSTUS is an open-source eukaryotic gene prediction tool that uses a generalized Hidden Markov Model and external evidence (ESTs, proteins, RNA‑Seq, comparative alignments) to produce accurate gene structures, UTRs and alternative transcripts.
BBTools is a fast, Java-based, open-source suite for preprocessing and analysing high-throughput sequencing data — offering read trimming, contamination filtering, mapping, error correction and k-mer tools to streamline NGS workflows.
BCFtools is a command‑line suite for calling, manipulating, filtering and annotating variants in VCF/BCF/gVCF formats. It’s designed for streaming pipelines, works with bgzip/tabix indexes, and integrates tightly with samtools/HTSlib for reproducible genomic workflows.
BEDTools is a fast, open-source toolkit for genome “arithmetic” — set operations on genomic intervals — enabling intersections, merges, coverage, proximity queries and other interval manipulations across common genomics formats.
Bioconda is a community-driven Conda channel that packages thousands of bioinformatics tools (and corresponding Docker/BioContainer images) for Linux and macOS, making life‑science software installation and reproducible deployment fast and consistent.
Bioconductor is an open-source ecosystem of R packages, tools, and containers for rigorous, reproducible analysis of high-throughput biological data—providing statistical methods, annotations, and infrastructure for genomics and related workflows.
BioContainers is a community-driven, open-source framework and registry that packages bioinformatics tools as portable software containers and Conda environments, with metadata and guidance to make tools reproducible and easy to deploy.
Biopython — an open-source Python library for computational molecular biology that supplies parsers, data structures and utilities for sequence analysis, alignments, phylogenetics, structural biology and BioSQL/BLAST integration.
Bracken estimates species- (or other taxonomic level-) level abundances from Kraken/Kraken2/KrakenUniq classification reports by redistributing reads according to k-mer-derived genome distributions, producing corrected abundance tables and kraken-style reports.
BUSCO evaluates completeness of genome assemblies, annotated gene sets and transcriptomes using evolutionarily informed single‑copy ortholog markers, delivering objective QC, annotation benchmarking and marker extraction for downstream analyses.
Canu is a hierarchical long‑read genome assembler for high‑noise single‑molecule data (PacBio, Oxford Nanopore) that performs overlap detection, error correction, trimming and assembly to produce accurate draft genomes.
