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A Swiss Army knife for genome arithmetic.

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

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

samtools/bcftools are a suite of tools for manipulating NGS data and can be used to call variants.

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.

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)

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

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

Genome mapping and spliced alignment of cDNA or amino acid sequences

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.

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

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.

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

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.

VerityMap is a tool for mapping long reads to assemblies of extra-long tandem repeats, producing SAM files and identifying potential heterozygous sites and assembly errors through analysis of rare k-mers. It supports PacBio HiFi and ONT reads and generates interactive HTML plots for variant analysis.

Create an index on a compressed text file.

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.