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fsom

A tiny C library for managing SOM (Self-Organizing Maps) neural networks

gaffy

GAF (graph alignment format) command line utility

gafpack

convert variation graph alignments to coverage maps over nodes

gatk-swe

gbwt

Substring index for paths in a graph

gbwtgraph

GBWT-based handle graph

gcsa2

BWT-based index for graphs

gencode

Scripts for working with data from GENCODE.

genotype

functions for exploring genotypes and genotype likelihoods

gfa-spec-walks

Graphical Fragment Assembly (GFA) Format Specification

gfaestus

GFA visualizer, GPU-accelerated using Vulkan

gimbricate

recompute GFA link overlaps

glia

a string to graph aligner

gprof-compare

compare call counts in two gprof profile outputs

graphappy

a variation graph-oriented fork of WhatsHap

guix-genomics

guix packages for bioinformatics software

handlegraph-cli

a template demonstrating how to load a variation graph (in GFA) into rs-handlegraph for processing

hapbin

Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)

hapviz

indel haplotype visualization on the command line from BAM files

hex2rgb

convert HEX to RGB color representation

hexygraph

a hexastore in C++ using leveldb

hgsvc

building variation graphs from hgsvc data

hhga

haplotypes genotypes and alleles example decision synthesizer

hla-zoo

genome variation graphs constructed from HLA GRCh38 ALTs

hpp_pangenome_resources

hpv_minion_analysis

Contains scripts used to analyze HPV samples sequenced on ONT minIONs.

htslib

C library for high-throughput sequencing data formats

iitii

Implicit Interval Tree with Interpolation Index

interleave-fastq

interleaves fastq files (also gzipped ones!)

intervalstab

interval stabbing (pointwise range lookup) using the FastStabbing algorithm