A versatile pairwise aligner for genomic and spliced nucleotide sequences

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Sequence-to-graph mapper and graph generator

🔬 BEDOPS: high-performance genomic feature operations

GenomeTools genome analysis system.

Reads simulator

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Finds SNP sites from a multi-FASTA alignment file

Tools for manipulating sequence graphs in the GFA and rGFA formats

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

De novo genome assembly and multisample variant calling

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Flexible genotype query among 30,000+ samples whole-genome

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

A WGS de novo assembler based on the FMD-index for large genomes

Model and predict short DNA sequence features with neural networks

Standalone C library for assembling Illumina short reads in small regions

Performs memory-efficient reservoir sampling on very large input files delimited by newlines