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minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequencesbwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)seqtk
Toolkit for processing sequences in FASTA/Q formatsbioawk
BWK awk modified for biological dataminigraph
Proof-of-concept seq-to-graph mapper and graph generatorminiasm
Ultrafast de novo assembly for long noisy reads (though having no consensus step)miniprot
Align proteins to genomes with splicing and frameshiftwgsim
Reads simulatorgfatools
Tools for manipulating sequence graphs in the GFA and rGFA formatsbiofast
Benchmarking programming languages/implementations for common tasks in Bioinformaticsreadfq
Fast multi-line FASTA/Q reader in several programming languageskmer-cnt
Code examples of fast and simple k-mer counters for tutorial purposespsmc
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) modelpangene
Constructing a pangenome gene graphksw2
Global alignment and alignment extensionbedtk
A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)fermikit
De novo assembly based variant calling pipeline for Illumina short readsminimap
This repo is DEPRECATED. Please use minimap2, the successor of minimap.yak
Yet another k-mer analyzerhickit
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-Cbgt
Flexible genotype query among 30,000+ samples whole-genomedipcall
Reference-based variant calling pipeline for a pair of phased haplotype assembliesunimap
A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignmentsrf
SRF: Satellite Repeat Finderfermi
A WGS de novo assembler based on the FMD-index for large genomesfermi-lite
Standalone C library for assembling Illumina short reads in small regionsdna-nn
Model and predict short DNA sequence features with neural networksropebwt2
Incremental construction of FM-index for DNA sequencesbfc
High-performance error correction for Illumina resequencing datatabtk
Toolkit for processing TAB-delimited formatgwfa
Proof-of-concept implementation of GWFA for sequence-to-graph alignmentCHM-eval
miniwfa
A reimplementation of the WaveFront Alignment algorithm at low memoryjstreeview
Interactive phylogenetic tree viewer/editorsamtools
This is *NOT* the official repository of samtools.etrf
Exact Tandem Repeat Finder (not a TRF replacement)bioseq-js
For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtmlref-gen
Human reference genome analysis setslv89
C implementation of the Landau-Vishkin algorithmpartig
An experimental tool to estimate the similarity between all pairs of contigsasub
A unified array job submitter for LSF, SGE/UGE and Slurmgffio
pre-pe
Preprocessing paired-end reads produced with experiment-specific protocolshapdip
The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina datacalN50
Compute N50/NG50 and auN/auNGsdust
Symmetric DUST for finding low-complexity regions in DNA sequencesvarcmp
The first CHM1 paper (Li, 2014)fermi2
misc
Useful small programslianti
Tools to process LIANTI sequence datartgeval
Wrapper for RTG's vcfeval; DEPRECATED!nasw
Dynamic programming for aa-to-nt alignment with affine gap, splicing and frameshiftpubLRasm
sgdp-fermi
FermiKit small variant calls for public SGDP samplesgfa1
This repo is deprecated. Please use gfatools instead.PortableCrystal
Portable Crystal binary distributions for Linux on x86_64foreign
Modified or extracted from other programstrimadap
Fast but inaccurate adapter trimmer for Illumina readslh3-snippets
unicall
A wrapper for calling small variants from human germline high-coverage single-sample Illumina datafastARG
Fast heuristic ARG constructionproot-wrapper
Demonstrating the PRoot programtreebest
TreeBeST: Tree Building guided by Species Treermaxcut
An experimental tool to find approximate max-cuts in a large graphbwa-docker
Minimal docker image for bwa. Not developed any more.sdg
EXPERIMENTAL implementation of side graphnaivepca
Naive PCA for genotype datamdust
mdust from DFCI Gene Indices Software Tools (archived for a historical record only)editdist-U85
Fast implementation of Ukkenon's O(ND) algorithm for computing edit distancelh3.github.com
libdivsufsort
Automatically exported from code.google.com/p/libdivsufsortmem-paper
Manuscript for BWA-MEMbcf2
Experimental bcftools port to support BCF2; DEPRECATED by htslib and htsboxthesis
PhD thesisropebwt
fermi-paper
The first fermi paper (Li, 2012)crlf
Concise Run-Length Format for small alphabets; DEPRECATEDpsnw
prototypecentos5-vm
Instructions on how to deploy CentOS 5 virtual machinesmag2gfa
DEPRECATED. Code has been moved to lh3/gfa1/miscibsget
Download files from Illumina BaseSpace (*OUTDATED* as BaseSpace has changed APIs)smtl-paper
Samtools statistics paper (Li, 2011)samtools-legacy
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