Glenn Hickey's Projects
Official home of genome aligner based upon notion of Cactus graphs
Convert progressive cactus database into a hal file
A place where random projects live
Generalization of Pair-HMM sequence aligner that uses a Pair-Tree Adjoining Grammar (TAG) for context sensitivity.
Simulate the evolution of a genome as represented by a pool of contigs
Tool to merge two vg graphs into a core graph
GBWT-based handle graph
BWT-based index for graphs
Graphical Fragment Assembly (GFA) Format Specification
A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
WDL scripts for the Giraffe/DeepVariant variant calling pipeline
Convert Glenn's internal graph variant format to VCF
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
Prototype code for converting HAL to Sequence/String/Side/? Graph
building variation graphs from hgsvc data
All code for reproducing reference graph bakeoff results
jenkins sandbox for playing with ci stuff
A C++ API to read and write kff files
recipe to make local ucsc genome browser instance for debugging hal / snake tracks
memory mapped multimap based on an in-place parallel binary sort and succinct indexes
Convert PAF with cg cigars to LASTZ cigars
Helper scripts used to build and debug Cactus pangenomes
Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
Some Compression streams (gzip, snappy, lz4) implementing the ZeroCopy Interface from Google(TM) protobuf 2.4.1
Fork of RED (REpeat Detector)
keep track of some scripts used to evaluate rgfa stuff