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

Proof-of-concept seq-to-graph mapper and graph generator

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

Reads simulator

Align proteins to genomes with splicing and frameshift

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)

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

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Global alignment and alignment extension

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

De novo assembly based variant calling pipeline for Illumina short reads

Yet another k-mer analyzer

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

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

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

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

Model and predict short DNA sequence features with neural networks

High-performance error correction for Illumina resequencing data

A reimplementation of the WaveFront Alignment algorithm at low memory

Exact Tandem Repeat Finder (not a TRF replacement)

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml