Pinned Repositories
cactus
Official home of genome aligner based upon notion of Cactus graphs
hal
Hierarchical Alignment Format
pg-stuff
Helper scripts used to build and debug Cactus pangenomes
progressiveCactus
Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
teHmm
Prototype code for identification of transposable elements in annotated DNA sequence using a HMM.
vg2maf
pangenome graph (vg) to multiple alignment (maf)
vg2sg
wgasv
Scripts for studying SVs via graphs constructed from whole-genome-alignment
toil-vg
Distributed and cloud computing framework for vg
vg
tools for working with genome variation graphs
glennhickey's Repositories
glennhickey/vg2maf
pangenome graph (vg) to multiple alignment (maf)
glennhickey/pg-stuff
Helper scripts used to build and debug Cactus pangenomes
glennhickey/wgasv
Scripts for studying SVs via graphs constructed from whole-genome-alignment
glennhickey/hgsvc
building variation graphs from hgsvc data
glennhickey/hal2sg
Prototype code for converting HAL to Sequence/String/Side/? Graph
glennhickey/panpatch
use pangenome of different assemblies for same sample to make patched assembly
glennhickey/rgfa
keep track of some scripts used to evaluate rgfa stuff
glennhickey/sv-genotyping-paper
glennhickey/CharlieSandbox
A place where random projects live
glennhickey/gbwtgraph
GBWT-based handle graph
glennhickey/GFA-spec
Graphical Fragment Assembly (GFA) Format Specification
glennhickey/gfakluge
A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
glennhickey/giraffe-dv-wdl
WDL scripts for the Giraffe/DeepVariant variant calling pipeline
glennhickey/glennhickey
glennhickey/glennhickey.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
glennhickey/kff-cpp-api
A C++ API to read and write kff files
glennhickey/local-browser
recipe to make local ucsc genome browser instance for debugging hal / snake tracks
glennhickey/mmmultimap
memory mapped multimap based on an in-place parallel binary sort and succinct indexes
glennhickey/paf2lastz
Convert PAF with cg cigars to LASTZ cigars
glennhickey/pg-pathcomp
glennhickey/red
Fork of RED (REpeat Detector)
glennhickey/repeatMaskerPipeline
glennhickey/sgExport
Some common code for converting into Side Graph format
glennhickey/sublinear-Li-Stephens
Calculates the probability of a haplotype given a population reference panel
glennhickey/swagg
glennhickey/taftools
playing around with some taf applications
glennhickey/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.
glennhickey/toil-vg
Home of the UC Santa Cruz Computational Genomics Lab's Toil-based VG pipeline
glennhickey/vg
tools for working with variant graphs
glennhickey/xg
xg0: a simpler xg index