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

Successor of bwa-mem for short-read alignment

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

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

Yet another k-mer analyzer

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

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

Reference-based variant calling pipeline for a pair of phased haplotype assemblies

SRF: Satellite Repeat Finder

De novo assembly based variant calling pipeline for Illumina short reads

This repo is DEPRECATED. Please use minimap2, the successor of minimap.

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

Incremental construction of FM-index for DNA sequences

Standalone C library for assembling Illumina short reads in small regions

Open Human Genome Library

Human reference genome analysis sets

Toolkit for processing TAB-delimited format

Scoring GT/AG sites for improving spliced alignment

Proof-of-concept implementation of GWFA for sequence-to-graph alignment

Exact Tandem Repeat Finder (not a TRF replacement)

A reimplementation of the WaveFront Alignment algorithm at low memory

Symmetric DUST for finding low-complexity regions in DNA sequences