Heng Li

Login: lh3

Company: Broad Institute

Location: Cambridge, MA, USA

Bio: null

Blog: http://lh3lh3.users.sourceforge.net

Blog: http://lh3lh3.users.sourceforge.net

Member of

2. Global Alliance for Genomics and Health

Repositories

alktk

null

asub

A unified array job submitter for LSF, SGE/UGE and Slurm

bcf2

Experimental bcftools port to support BCF2; DEPRECATED by htslib and htsbox

bedtools2

A powerful toolset for genome arithmetic.

bfc

High-performance error correction for Illumina resequencing data

bgt

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

bhtsne

Barnes-Hut t-SNE

bioawk

BWK awk modified for biological data

bioconda-recipes

Conda recipes for the bioconda channel.

BioD

Bioinformatics library in D. (utils for working with SAM, BAM, SFF formats)

bioseq-js

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

bwa

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

bwa-docker

Minimal docker image for bwa. Not developed any more.

centos5-vm

Instructions on how to deploy CentOS 5 virtual machines

CHM-eval

null

crlf

Concise Run-Length Format for small alphabets; DEPRECATED

fastARG

Fast heuristic ARG construction

fermi

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

fermi2

null

fermikit

De novo assembly based variant calling pipeline for Illumina short reads

fermi-lite

Standalone C library for assembling Illumina short reads in small regions

fermi-paper

null

foreign

Modified or extracted from other programs

gfa1

Library and command-line tool to manipulate assembly graph in the GFA format

gfatools

DEPRECATED by lh3/gfa1.

gnuplot-colorbrewer

ColorBrewer color schemes for gnuplot

hapdip

The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data

htsbox

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

htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

ibsget

Download files from Illumina BaseSpace

igv.js

Lightweight html5 version of the Integrative Genomics Viewer

Jellyfish

A fast multi-threaded k-mer counter

ksw2

Global alignment and alignment extension

lh3.github.com

null

lh3-snippets

null

lianti

Tools to process LIANTI sequence data

libdivsufsort

Automatically exported from code.google.com/p/libdivsufsort

mag2gfa

DEPRECATED. Code has been moved to lh3/gfa1/misc

markdown-editor

Live (Github-flavored) Markdown Editor

math-parser-benchmark-project

Automatically exported from code.google.com/p/math-parser-benchmark-project

mdust

mdust from DFCI Gene Indices Software Tools (archived for a historical record only)

mem-paper

Manuscript for BWA-MEM

miniasm

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

minimap

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

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

misc

Useful small programs

naivepca

Naive PCA for genotype data

nuc_dynamics

Particle dynamics and simulated annealing for chromosome structure calculation

null-buildpack

a heroku buildpack that runs executables

nvbio

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.

PBSIM-PacBio-Simulator

This is an updated mirror of the original PacBio Read Simulator

pre-pe

Preprocessing paired-end reads produced with experiment-specific protocols

proot-wrapper

Demonstrating the PRoot program

psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

quartz

A fork of Quartz (QUAlity score Reduction at Terabyte scale)

readfq

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

ropebwt

null

ropebwt2

Incremental construction of FM-index for DNA sequences

Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

rtgeval

Wrapper for RTG's vcfeval

samblaster

samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.

samtools

This is *NOT* the official repository of samtools.

samtools-legacy

For testing only. DON'T USE!

schemas

The upstream repo has been deprecated, so is this one.

sdg

EXPERIMENTAL implementation of side graph

seqtk

Toolkit for processing sequences in FASTA/Q formats

sff2fastq

extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output

sgdp-fermi

FermiKit small variant calls for public SGDP samples

smtl-paper

null

tabtk

Toolkit for processing TAB-delimited format

thesis

PhD thesis

treebest

TreeBeST: Tree Building guided by Species Tree

trimadap

Fast but inaccurate adapter trimmer for Illumina reads

unicall

A wrapper for calling small variants from human germline high-coverage single-sample Illumina data

varcmp

null

wgsim

Reads simulator

Commits To