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DFCI & Harvard University
- Boston, MA, USA
- http://liheng.org
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ropebwt3 Public
Construction and utility of BWT for DNA string sets
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bwa Public
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
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minimap2 Public
A versatile pairwise aligner for genomic and spliced nucleotide sequences
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mssa-bench Public
Evaluating the performance of multi-string SA construction
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minisv Public
Lightweight mosaic/somatic SV caller for long reads (WIP)
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ropebwt2 Public
Incremental construction of FM-index for DNA sequences
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gwfa Public
Proof-of-concept implementation of GWFA for sequence-to-graph alignment
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pangene Public
Constructing a pangenome gene graph
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bedtk Public
A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
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cgranges Public
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
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miniwfa Public
A reimplementation of the WaveFront Alignment algorithm at low memory
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minigraph Public
Sequence-to-graph mapper and graph generator
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miniprot Public
Align proteins to genomes with splicing and frameshift
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minipileup Public
Simple pileup-based variant caller
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zenodo-upload Public
Forked from jhpoelen/zenodo-uploadupload big files to Zenodo using cURL, jq and bash
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gfatools Public
Tools for manipulating sequence graphs in the GFA and rGFA formats
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miniasm Public
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
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seqtk Public
Toolkit for processing sequences in FASTA/Q formats
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calN50 Public
Compute N50/NG50 and auN/auNG
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sdust Public
Symmetric DUST for finding low-complexity regions in DNA sequences
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htsbox Public
Forked from samtools/htslibMy experimental tools on top of htslib. NOT OFFICIAL!!!
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jstreeview Public
Interactive phylogenetic tree viewer/editor
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ksw2 Public
Global alignment and alignment extension
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ggml Public
Forked from ggerganov/ggmlTensor library for machine learning
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