Purdue University

Basic Local Alignment Search Tool. BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.

BlobTools is a modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.

Bmge is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference.

Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library.

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.

Brass is used to analyze one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints.

Breseq is a computational pipeline for the analysis of short-read re-sequencing data.

BUSCO (Benchmarking sets of Universal Single-Copy Orthologs) provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.

Bustools is a program for manipulating BUS files for single cell RNA-Seq datasets.

BWA (Burrows-Wheeler Aligner) is a fast, accurate, memory-efficient aligner for short and long sequencing reads.

Bwameth is a tool for fast and accurante alignment of BS-Seq reads.

bzip2 is a freely available, patent free high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques the PPM family of statistical compressors, whilst being around twice as fast at compression and six times faster at decompression.

Cactus is a reference-free whole-genome multiple alignment program.

Cafe is a computational tool for the study of gene family evolution.

Caffe is a deep learning framework made with expression, speed, and modularity in mind.

Canu is a single molecule sequence assembler for genomes large and small.