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minimap2 Public
A versatile pairwise aligner for genomic and spliced nucleotide sequences
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phycfg Public
Modeling phylogenetic trees with Stochastic Context-Free Grammar (SCFG)
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longdust Public
Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome
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ropebwt3 Public
BWT construction and search
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hickit Public
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
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miniprot Public
Align proteins to genomes with splicing and frameshift
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yak Public
Yet another k-mer analyzer
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open-data-registry Public
Forked from awslabs/open-data-registryA registry of publicly available datasets on AWS
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gfatools Public
Tools for manipulating sequence graphs in the GFA and rGFA formats
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psmc Public
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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minisv Public
Lightweight mosaic/somatic SV caller for long reads (WIP)
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lcg Public
Forked from ddiazdom/lcgEfficient, parallel compression for terabyte-scale data
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htsbox Public
Forked from samtools/htslibMy experimental tools on top of htslib. NOT OFFICIAL!!!
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panmask Public
Easy genomic regions for short-read variant calling
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bedtk Public
A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
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pangene Public
Constructing a pangenome gene graph
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minigraph Public
Sequence-to-graph mapper and graph generator
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TRF-mod Public
Forked from Benson-Genomics-Lab/TRFTandem Repeats Finder: a program to analyze DNA sequences
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sdust Public
Symmetric DUST for finding low-complexity regions in DNA sequences
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minigff Public
Parsing and evaluating gene annotation and spliced alignment
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miniasm Public
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
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