Beast code in Giters

Heng Li's repositories

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Language:CNOASSERTION1746 87 1106

bwa

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

Language:CGPL-3.01501 107 301

seqtk

Toolkit for processing sequences in FASTA/Q formats

Language:CMIT1360 62 171

minigraph

Sequence-to-graph mapper and graph generator

Language:CMIT402 28 109

miniprot

Align proteins to genomes with splicing and frameshift

Language:CMIT313 7 56

miniasm

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

Language:TeXMIT302 29 86

gfatools

Tools for manipulating sequence graphs in the GFA and rGFA formats

Language:C206 17 33

cgranges

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

Language:CMIT165 12 10

pangene

Constructing a pangenome gene graph

Language:C158 8 9

bedtk

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

Language:CMIT134 8 1

ksw2

Global alignment and alignment extension

Language:CNOASSERTION127 14 23

yak

Yet another k-mer analyzer

Language:CMIT110 8 24

srf

SRF: Satellite Repeat Finder

Language:TeXMIT82 5 17

minipileup

Simple pileup-based variant caller

Language:C79 4 15

ropebwt2

Incremental construction of FM-index for DNA sequences

Language:TeXMIT67 11 6

gwfa

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

Language:CMIT55 40

htsbox

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

Language:CNOASSERTION52 70

miniwfa

A reimplementation of the WaveFront Alignment algorithm at low memory

Language:CMIT49 5 4

jstreeview

Interactive phylogenetic tree viewer/editor

Language:JavaScript46 20

ref-gen

Human reference genome analysis sets

Language:Makefile44 3 1

calN50

Compute N50/NG50 and auN/auNG

Language:JavaScript31 40

gffio

Language:C31 40

sdust

Symmetric DUST for finding low-complexity regions in DNA sequences

Language:C31 4 3

minisv

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

Language:JavaScriptMIT24 3 1

lh3.github.com

Language:TeX9 40

ropebwt3

Construction and utility of BWT for DNA string sets

Language:CNOASSERTION9 10

zenodo-upload

upload big files to Zenodo using cURL, jq and bash

Language:ShellMIT2 20

ggml

Tensor library for machine learning

Language:CMIT1 10

mssa-bench

Evaluating the performance of multi-string SA construction

Language:C100

BMIF-201

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