lh3

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

Toolkit for processing sequences in FASTA/Q formats

BWK awk modified for biological data

Sequence-to-graph mapper and graph generator

Align proteins to genomes with splicing and frameshift

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Successor of bwa-mem for short-read alignment

Reads simulator

Tools for manipulating sequence graphs in the GFA and rGFA formats

Constructing a pangenome gene graph

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Fast multi-line FASTA/Q reader in several programming languages

Code examples of fast and simple k-mer counters for tutorial purposes

Yet another k-mer analyzer

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

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

Global alignment and alignment extension

BWT construction and search

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

De novo assembly based variant calling pipeline for Illumina short reads

Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome

Simple pileup-based variant caller

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

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

Model and predict short DNA sequence features with neural networks

High-performance error correction for Illumina resequencing data

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

Standalone C library for assembling Illumina short reads in small regions