Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.
Count bases in BAM/CRAM files
Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files
BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.
C++ API & command-line toolkit for working with BAM data
Barrnap predicts the location of ribosomal RNA genes in genomes. (bacteria, archaea, metazoan mitochondria and eukaryotes.)
BatMeth2: An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.
BBMap is a short read aligner, as well as various other bioinformatic tools.
bc is an arbitrary precision numeric processing language.
A Python library to read and write Generic Feature Format (GFF).
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
The Illumina bcl2fastq2 Conversion Software demultiplexes sequencing data and converts base call (BCL) files into FASTQ files.
general purpose library for evaluating the likelihood of sequence evolution on trees
BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC
BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
High-performance genomic feature operations.
A powerful toolset for genome arithmetic
Trim, circularise and orient long read bacterial genome assemblies.
Highly parallel construction and indexing of colored and compacted de Bruijn graphs
Biosynthetic Genes Similarity Clustering and Prospecting Engine.
Smart VCF parser
BWK awk modified for biological data
CloudMan and Galaxy API library
Accurate, high-resolution sample inference from amplicon sequencing data
SeqStat is a package that contains tools to generate stats from a FastQ file, merge those stats for multiple samples, and validate the generated stats files.
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away.
routines that provide standard building blocks for performing basic vector and matrix operations
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
BMGE (Block Mapping and Gathering with Entropy) is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference.
bmtool is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
Statistical and novel interactive HTML plots for Python
free peer-reviewed portable C++ source libraries
An ultrafast memory-efficient short read aligner
Fast and sensitive gapped read alignment
Bio++ is a set of C++ libraries for Bioinformatics.
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.
BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.
BRAKER3 enables the usage of RNA-seq and protein data in a fully automated pipeline to train and predict highly reliable genes with GeneMark-ETP and AUGUSTUS. The result of the pipeline is the combined gene set of both gene prediction tools, which only contains genes with very high support from extrinsic evidence.
A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data.
Assessment of assembly completeness using Universal Single Copy Orthologs
bustools is a program for manipulating BUS files for single cell RNA-Seq datasets.
The BWA read mapper.
The next version of bwa-mem