glennhickey

progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

vg2maf

pangenome graph (vg) to multiple alignment (maf)

pg-stuff

Helper scripts used to build and debug Cactus pangenomes

wgasv

Scripts for studying SVs via graphs constructed from whole-genome-alignment

hgsvc

building variation graphs from hgsvc data

cactus

Official home of genome aligner based upon notion of Cactus graphs

cactus2hal

Convert progressive cactus database into a hal file

hal2sg

Prototype code for converting HAL to Sequence/String/Side/? Graph

rgfa

keep track of some scripts used to evaluate rgfa stuff

sv-genotyping-paper

CharlieSandbox

A place where random projects live

gbwtgraph

GBWT-based handle graph

GFA-spec

Graphical Fragment Assembly (GFA) Format Specification

gfakluge

A C++ library and utilities for manipulating the Graphical Fragment Assembly format.

giraffe-dv-wdl

WDL scripts for the Giraffe/DeepVariant variant calling pipeline

glennhickey

glennhickey.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

local-browser

recipe to make local ucsc genome browser instance for debugging hal / snake tracks

mmmultimap

memory mapped multimap based on an in-place parallel binary sort and succinct indexes

paf2lastz

Convert PAF with cg cigars to LASTZ cigars

pg-pathcomp

red

Fork of RED (REpeat Detector)

repeatMaskerPipeline

sgExport

Some common code for converting into Side Graph format

swagg

taftools

playing around with some taf applications

toil

Python based pipeline management software for clusters that makes running recursive and dynamically scheduled computations straightforward. So far works with gridEngine, lsf, parasol and on multi-core machines.

toil-vg

Home of the UC Santa Cruz Computational Genomics Lab's Toil-based VG pipeline

vg

tools for working with variant graphs

xg

xg0: a simpler xg index