lh3/TRF-mod Fork of Benson-Genomics-Lab/TRF

Tandem Repeats Finder: a program to analyze DNA sequences

Language: C - Size: 867 KB - Last synced at: about 22 hours ago - Pushed at: about 22 hours ago - Stars: 16 - Forks: 2

lh3/bwa

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

Language: C - Size: 1.7 MB - Last synced at: 4 days ago - Pushed at: 4 months ago - Stars: 1,637 - Forks: 565

lh3/miniasm

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

Language: TeX - Size: 855 KB - Last synced at: 11 days ago - Pushed at: 12 days ago - Stars: 325 - Forks: 69

lh3/minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Language: C - Size: 1.57 MB - Last synced at: 13 days ago - Pushed at: about 1 month ago - Stars: 1,998 - Forks: 440

lh3/minisplice

Scoring GT/AG sites for improving spliced alignment

Language: C - Size: 557 KB - Last synced at: 14 days ago - Pushed at: 15 days ago - Stars: 45 - Forks: 3

lh3/panmask

Easy genomic regions for short-read variant calling

Language: TeX - Size: 37.1 KB - Last synced at: 15 days ago - Pushed at: 16 days ago - Stars: 29 - Forks: 0

lh3/ropebwt3

BWT construction and search

Language: C - Size: 360 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 116 - Forks: 6

lh3/minigff

Parsing and evaluating gene annotation and spliced alignment

Language: JavaScript - Size: 135 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 22 - Forks: 1

lh3/miniprot

Align proteins to genomes with splicing and frameshift

Language: C - Size: 361 KB - Last synced at: 18 days ago - Pushed at: 19 days ago - Stars: 375 - Forks: 21

lh3/pangene

Constructing a pangenome gene graph

Language: C - Size: 339 KB - Last synced at: 8 days ago - Pushed at: about 2 months ago - Stars: 193 - Forks: 12

lh3/bioawk

BWK awk modified for biological data

Language: C - Size: 127 KB - Last synced at: 4 days ago - Pushed at: almost 3 years ago - Stars: 624 - Forks: 119

lh3/minigraph

Sequence-to-graph mapper and graph generator

Language: C - Size: 928 KB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 450 - Forks: 39

lh3/seqtk

Toolkit for processing sequences in FASTA/Q formats

Language: C - Size: 179 KB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 1,475 - Forks: 315

lh3/srf

SRF: Satellite Repeat Finder

Language: TeX - Size: 180 KB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 96 - Forks: 6

lh3/ref-gen

Human reference genome analysis sets

Language: Makefile - Size: 4.88 KB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 53 - Forks: 3

lh3/bedtk

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

Language: C - Size: 451 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 140 - Forks: 17

lh3/bgt

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

Language: C - Size: 303 KB - Last synced at: about 2 months ago - Pushed at: almost 6 years ago - Stars: 95 - Forks: 10

lh3/wgsim

Reads simulator

Language: C - Size: 128 KB - Last synced at: 2 months ago - Pushed at: almost 4 years ago - Stars: 275 - Forks: 90

lh3/sdust

Symmetric DUST for finding low-complexity regions in DNA sequences

Language: C - Size: 10.7 KB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 42 - Forks: 9

lh3/minisv

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

Language: JavaScript - Size: 565 KB - Last synced at: about 2 months ago - Pushed at: 8 months ago - Stars: 29 - Forks: 3

lh3/minipileup

Simple pileup-based variant caller

Language: C - Size: 120 KB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 89 - Forks: 9

lh3/cgranges

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

Language: C - Size: 81.1 KB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 167 - Forks: 18

lh3/calN50

Compute N50/NG50 and auN/auNG

Language: JavaScript - Size: 6.84 KB - Last synced at: 3 months ago - Pushed at: almost 2 years ago - Stars: 32 - Forks: 2

lh3/hickit

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

Language: C - Size: 4.5 MB - Last synced at: 3 months ago - Pushed at: over 4 years ago - Stars: 107 - Forks: 11

lh3/gfatools

Tools for manipulating sequence graphs in the GFA and rGFA formats

Language: C - Size: 542 KB - Last synced at: 3 months ago - Pushed at: 12 months ago - Stars: 225 - Forks: 21

lh3/etrf

Exact Tandem Repeat Finder (not a TRF replacement)

Language: C - Size: 10.7 KB - Last synced at: 3 months ago - Pushed at: almost 6 years ago - Stars: 49 - Forks: 2

lh3/psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Language: C - Size: 97.7 KB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 166 - Forks: 60

lh3/lh3.github.com

Language: TeX - Size: 6.2 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 9 - Forks: 5

lh3/biofast

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Language: C - Size: 124 KB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 185 - Forks: 26

lh3/yak

Yet another k-mer analyzer

Language: C - Size: 85.9 KB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 133 - Forks: 9

lh3/unicall

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

Language: Perl - Size: 14.6 KB - Last synced at: 3 months ago - Pushed at: about 6 years ago - Stars: 14 - Forks: 5

lh3/readfq

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

Language: C - Size: 17.6 KB - Last synced at: about 2 months ago - Pushed at: about 4 years ago - Stars: 176 - Forks: 58

lh3/rankbench

Testing rank calculation on BWT (not for endusers)

Language: C - Size: 26.4 KB - Last synced at: 3 months ago - Pushed at: 11 months ago - Stars: 4 - Forks: 0

lh3/ksw2

Global alignment and alignment extension

Language: C - Size: 189 KB - Last synced at: 3 months ago - Pushed at: about 2 years ago - Stars: 131 - Forks: 26

lh3/kmer-cnt

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

Language: C++ - Size: 81.1 KB - Last synced at: 3 months ago - Pushed at: over 5 years ago - Stars: 168 - Forks: 15

lh3/mssa-bench

Evaluating the performance of multi-string SA construction

Language: C - Size: 301 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 1

lh3/msais-lite

Constructing the genernalized suffix array of a string set

Language: C - Size: 26.4 KB - Last synced at: about 2 months ago - Pushed at: 5 months ago - Stars: 9 - Forks: 0

lh3/dipcall

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

Language: JavaScript - Size: 23.4 KB - Last synced at: 3 months ago - Pushed at: about 4 years ago - Stars: 100 - Forks: 10

lh3/dna-nn

Model and predict short DNA sequence features with neural networks

Language: C - Size: 171 KB - Last synced at: 3 months ago - Pushed at: about 6 years ago - Stars: 75 - Forks: 10

lh3/proot-wrapper

Demonstrating the PRoot program

Language: Perl - Size: 7.81 KB - Last synced at: 3 months ago - Pushed at: about 9 years ago - Stars: 11 - Forks: 0

lh3/bioseq-js

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

Language: HTML - Size: 16.6 KB - Last synced at: 5 months ago - Pushed at: almost 6 years ago - Stars: 38 - Forks: 16

lh3/samtools

This is *NOT* the official repository of samtools.

Language: C - Size: 1.15 MB - Last synced at: 3 months ago - Pushed at: about 8 years ago - Stars: 47 - Forks: 39

lh3/fermi

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

Language: C - Size: 1.95 MB - Last synced at: 4 days ago - Pushed at: over 11 years ago - Stars: 74 - Forks: 15

lh3/tabtk

Toolkit for processing TAB-delimited format

Language: C - Size: 37.1 KB - Last synced at: 4 months ago - Pushed at: 10 months ago - Stars: 62 - Forks: 12

lh3/pubLRasm

Size: 5.86 KB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 17 - Forks: 1

lh3/ropebwt2

Incremental construction of FM-index for DNA sequences

Language: TeX - Size: 195 KB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 70 - Forks: 5

lh3/unimap

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

Language: C - Size: 487 KB - Last synced at: 3 months ago - Pushed at: over 4 years ago - Stars: 88 - Forks: 4

lh3/gwfa

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

Language: C - Size: 292 KB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 57 - Forks: 1

lh3/minimap 📦

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

Language: C - Size: 105 KB - Last synced at: 3 months ago - Pushed at: almost 8 years ago - Stars: 105 - Forks: 29

lh3/nasw

Dynamic programming for aa-to-nt alignment with affine gap, splicing and frameshift

Language: C - Size: 96.7 KB - Last synced at: 3 months ago - Pushed at: 10 months ago - Stars: 19 - Forks: 0

lh3/fermikit

De novo assembly based variant calling pipeline for Illumina short reads

Language: TeX - Size: 7.45 MB - Last synced at: 4 days ago - Pushed at: over 4 years ago - Stars: 108 - Forks: 21

lh3/libdivsufsort

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

Language: C - Size: 242 KB - Last synced at: 4 days ago - Pushed at: over 10 years ago - Stars: 7 - Forks: 4

lh3/CHM-eval

Language: TeX - Size: 524 KB - Last synced at: 5 months ago - Pushed at: about 5 years ago - Stars: 53 - Forks: 8

lh3/bfc

High-performance error correction for Illumina resequencing data

Language: TeX - Size: 514 KB - Last synced at: 5 months ago - Pushed at: about 9 years ago - Stars: 69 - Forks: 13

lh3/pre-pe

Preprocessing paired-end reads produced with experiment-specific protocols

Language: C - Size: 42 KB - Last synced at: 10 days ago - Pushed at: about 7 years ago - Stars: 32 - Forks: 2

lh3/asub

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

Language: Perl - Size: 16.6 KB - Last synced at: 24 days ago - Pushed at: 10 months ago - Stars: 32 - Forks: 16

lh3/BMIF-201

Language: TeX - Size: 46.9 KB - Last synced at: about 2 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

lh3/gffio

Language: C - Size: 232 KB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 32 - Forks: 1

lh3/treebest

TreeBeST: Tree Building guided by Species Tree

Language: C - Size: 404 KB - Last synced at: 3 months ago - Pushed at: over 14 years ago - Stars: 14 - Forks: 12

lh3/partig

An experimental tool to estimate the similarity between all pairs of contigs

Language: C - Size: 113 KB - Last synced at: 3 months ago - Pushed at: over 4 years ago - Stars: 35 - Forks: 1

lh3/miniwfa

A reimplementation of the WaveFront Alignment algorithm at low memory

Language: C - Size: 197 KB - Last synced at: 12 days ago - Pushed at: about 1 year ago - Stars: 49 - Forks: 4

lh3/sgdp-fermi

FermiKit small variant calls for public SGDP samples

Size: 4.88 KB - Last synced at: 5 months ago - Pushed at: almost 9 years ago - Stars: 17 - Forks: 0

lh3/fermi2

Language: C - Size: 191 KB - Last synced at: 3 months ago - Pushed at: about 4 years ago - Stars: 26 - Forks: 2

lh3/bhtsne Fork of lvdmaaten/bhtsne

Barnes-Hut t-SNE

Language: C++ - Size: 104 KB - Last synced at: about 1 year ago - Pushed at: almost 9 years ago - Stars: 5 - Forks: 1

lh3/misc

Useful small programs

Language: C - Size: 228 KB - Last synced at: 3 months ago - Pushed at: over 12 years ago - Stars: 26 - Forks: 10

lh3/hifiasm-meta Fork of xfengnefx/hifiasm-meta

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Size: 13.2 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 17 - Forks: 2

lh3/htsbox Fork of samtools/htslib

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

Language: C - Size: 6.57 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 52 - Forks: 7

lh3/fermi-lite

Standalone C library for assembling Illumina short reads in small regions

Language: C - Size: 277 KB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 72 - Forks: 23

lh3/rtgeval 📦

Wrapper for RTG's vcfeval; DEPRECATED!

Language: Shell - Size: 5.74 MB - Last synced at: about 1 year ago - Pushed at: over 9 years ago - Stars: 21 - Forks: 2

lh3/zenodo-upload Fork of jhpoelen/zenodo-upload

upload big files to Zenodo using cURL, jq and bash

Language: Shell - Size: 4.88 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

lh3/lv89 📦

C implementation of the Landau-Vishkin algorithm

Language: C++ - Size: 117 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 35 - Forks: 0

lh3/chromap Fork of haowenz/chromap

Fast alignment and preprocessing of chromatin profiles

Size: 43.6 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0

lh3/jstreeview

Interactive phylogenetic tree viewer/editor

Language: JavaScript - Size: 31.3 KB - Last synced at: 3 months ago - Pushed at: about 2 years ago - Stars: 46 - Forks: 3

lh3/hapdip

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

Language: JavaScript - Size: 124 KB - Last synced at: 3 months ago - Pushed at: over 7 years ago - Stars: 30 - Forks: 5

lh3/lianti

Tools to process LIANTI sequence data

Language: C - Size: 203 KB - Last synced at: 3 months ago - Pushed at: over 6 years ago - Stars: 23 - Forks: 6

lh3/PortableCrystal

Portable Crystal binary distributions for Linux on x86_64

Size: 1.95 KB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 15 - Forks: 1

lh3/mdust 📦

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

Language: C - Size: 105 KB - Last synced at: about 1 year ago - Pushed at: over 10 years ago - Stars: 10 - Forks: 3

lh3/fastARG 📦

Fast heuristic ARG construction

Language: C - Size: 39.1 KB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 12 - Forks: 4

lh3/mag2gfa 📦

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

Language: C - Size: 14.6 KB - Last synced at: about 1 year ago - Pushed at: about 9 years ago - Stars: 2 - Forks: 1

lh3/bwa-docker 📦

Minimal docker image for bwa. Not developed any more.

Size: 648 KB - Last synced at: about 1 year ago - Pushed at: over 10 years ago - Stars: 11 - Forks: 4

lh3/crlf 📦

Concise Run-Length Format for small alphabets; DEPRECATED

Language: C - Size: 152 KB - Last synced at: about 1 year ago - Pushed at: about 11 years ago - Stars: 3 - Forks: 0

lh3/schemas Fork of ga4gh/ga4gh-schemas 📦

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

Language: Python - Size: 901 KB - Last synced at: about 1 year ago - Pushed at: almost 10 years ago - Stars: 0 - Forks: 0

lh3/bcf2 📦

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

Language: C - Size: 168 KB - Last synced at: about 1 year ago - Pushed at: over 12 years ago - Stars: 6 - Forks: 0

lh3/thesis 📦

PhD thesis

Language: TeX - Size: 652 KB - Last synced at: about 1 year ago - Pushed at: over 11 years ago - Stars: 5 - Forks: 3

lh3/quartz Fork of yunwilliamyu/quartz 📦

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

Language: C - Size: 176 KB - Last synced at: about 1 year ago - Pushed at: over 10 years ago - Stars: 0 - Forks: 0

lh3/alktk 📦

Failed experiment. Archived for a historical record.

Language: C - Size: 133 KB - Last synced at: about 1 year ago - Pushed at: almost 12 years ago - Stars: 0 - Forks: 0

lh3/fermi-paper 📦

The first fermi paper (Li, 2012)

Size: 162 KB - Last synced at: about 1 year ago - Pushed at: about 13 years ago - Stars: 3 - Forks: 1

lh3/smtl-paper 📦

Samtools statistics paper (Li, 2011)

Language: Lua - Size: 789 KB - Last synced at: about 1 year ago - Pushed at: over 13 years ago - Stars: 1 - Forks: 0

lh3/varcmp 📦

The first CHM1 paper (Li, 2014)

Language: TeX - Size: 24 MB - Last synced at: about 1 year ago - Pushed at: about 11 years ago - Stars: 25 - Forks: 4

lh3/ibsget 📦

Download files from Illumina BaseSpace (*OUTDATED* as BaseSpace has changed APIs)

Language: C - Size: 1.21 MB - Last synced at: about 1 year ago - Pushed at: over 10 years ago - Stars: 2 - Forks: 0

lh3/gfa1 📦

This repo is deprecated. Please use gfatools instead.

Language: C - Size: 69.3 KB - Last synced at: about 1 year ago - Pushed at: almost 7 years ago - Stars: 15 - Forks: 3

lh3/gdown.pl Fork of circulosmeos/gdown.pl

Google Drive direct download of big files

Size: 25.4 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

lh3/GFA-spec Fork of GFA-spec/GFA-spec

Graphical Fragment Assembly (GFA) Format Specification

Size: 1.09 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

lh3/trimadap

Fast but inaccurate adapter trimmer for Illumina reads

Language: C - Size: 20.5 KB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 14 - Forks: 8

lh3/psnw

prototype

Language: C - Size: 8.79 KB - Last synced at: 5 months ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

lh3/editdist-U85

Fast implementation of Ukkenon's O(ND) algorithm for computing edit distance

Language: C - Size: 25.4 KB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 9 - Forks: 1

lh3/Jellyfish Fork of gmarcais/Jellyfish

A fast multi-threaded k-mer counter

Language: C++ - Size: 3.2 MB - Last synced at: about 1 year ago - Pushed at: over 10 years ago - Stars: 3 - Forks: 4

lh3/HPP_Year1_Assemblies Fork of human-pangenomics/HPP_Year1_Assemblies

Assemblies from HPP Year 1 production

Size: 1.12 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

lh3/klib.nim

Experimental getopt, gzip reader, FASTA/Q parser and interval queries in nim-lang

Language: Nim - Size: 11.7 KB - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 32 - Forks: 1

lh3/mem-paper

Manuscript for BWA-MEM

Size: 387 KB - Last synced at: 5 months ago - Pushed at: almost 12 years ago - Stars: 6 - Forks: 2