Heng Li

minimap2. A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

seqtk. Toolkit for processing sequences in FASTA/Q formats

bioawk. BWK awk modified for biological data

minigraph. Sequence-to-graph mapper and graph generator

miniprot. Align proteins to genomes with splicing and frameshift

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

wgsim. Reads simulator

gfatools. Tools for manipulating sequence graphs in the GFA and rGFA formats

pangene. Constructing a pangenome gene graph

psmc. Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

biofast. Benchmarking programming languages/implementations for common tasks in Bioinformatics

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

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

yak. Yet another k-mer analyzer

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

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

ksw2. Global alignment and alignment extension

ropebwt3. BWT construction and search

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

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

fermikit. De novo assembly based variant calling pipeline for Illumina short reads

srf. SRF: Satellite Repeat Finder

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

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

minipileup. Simple pileup-based variant caller

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

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

dna-nn. Model and predict short DNA sequence features with neural networks

bfc. High-performance error correction for Illumina resequencing data

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

ropebwt2. Incremental construction of FM-index for DNA sequences

fermi-lite. Standalone C library for assembling Illumina short reads in small regions

tabtk. Toolkit for processing TAB-delimited format

ref-gen. Human reference genome analysis sets

htsbox. My experimental tools on top of htslib. NOT OFFICIAL!!!

minisplice. Scoring GT/AG sites for improving spliced alignment

miniwfa. A reimplementation of the WaveFront Alignment algorithm at low memory

minisv. Lightweight mosaic/somatic SV caller for long reads (WIP)

pre-pe. Preprocessing paired-end reads produced with experiment-specific protocols

gffio. C

fermi2. C

lianti. Tools to process LIANTI sequence data

rtgeval. Wrapper for RTG's vcfeval; DEPRECATED!

sgdp-fermi. FermiKit small variant calls for public SGDP samples