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A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.

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.

A compressor of common genomic file formats (BAM, CRAM, FASTQ, VCF etc).

Fast and accurate protein structure search using a learned 3Di structural alphabet (VQ-VAE) that discretizes tertiary interactions into structural tokens, enabling protein-universe-scale structural alignment at sequence-search speeds (4-5 orders of magnitude faster than DALI/TM-align) and underpinning many AI4S tools such as SaProt, ESMAtlas search, and AFDB clustering pipelines (Steinegger Lab, Nature Biotechnology 2023)

metilene³ is a computational tool for identifying Differentially Methylated Regions (DMRs) across multiple conditions, supporting both supervised and unsupervised analyses, and enables the construction of Differentially Methylated Trees for epigenetic relationship inference and sample clustering.

SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.

The main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.

Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.

the wavefront alignment algorithm (WFA) which expoit sequence similarity to speed up alignment

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

A Swiss Army knife for genome arithmetic.

Minimap2 is an pairwise aligner for genomic and spliced nucleotide sequences. It can perform the assembly-to-assembly alignment, and works with gzip'd FASTQ, FASTA formats. It also finds overlaps between long-reads.

De novo assembler for single molecule sequencing reads using repeat graphs.

BWA-MEM drop-in replacement: 2-3x faster, 2-5x cheaper, 100% identical output on standard CPUs.

lumpy: a general probabilistic framework for structural variant discovery.

Pairwise SNP distance matrix from a FASTA sequence alignment

SIMD C library for global, semi-global, and local pairwise sequence alignments

Minigraph is a sequence-to-graph mapper and graph constructor. For graph generation, it aligns a query sequence against a sequence graph and incrementally augments an existing graph with long query subsequences diverged from the graph.

Toolkit for processing sequences in FASTA/Q formats.

A database system designed to store, organize, and manage large-scale nucleotide sequencing read data (like PacBio reads) for the Dazzler genome assembler

A fuzzy Bruijn graph approach to long noisy reads assembly

Displaying sequence statistics for next-generation sequencing.

Create an index on a compressed text file.

Standalone C library for assembling Illumina short reads in small regions

FASTQ/A short-reads pre-processing tools: Demultiplexing, trimming, clipping, quality filtering, and masking utilities.

**Comes with samtools!** - Reads simulator.

Finds SNP sites from a multi-FASTA alignment file.

A wee tool for random access into BGZF files.

Comprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX.