Glenn Hickey

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

vg2maf. pangenome graph (vg) to multiple alignment (maf)

panpatch. use pangenome of different assemblies for same sample to make patched assembly

teHmm. Prototype code for identification of transposable elements in annotated DNA sequence using a HMM.

pg-stuff. Helper scripts used to build and debug Cactus pangenomes

vg2sg. C++

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

context. Generalization of Pair-HMM sequence aligner that uses a Pair-Tree Adjoining Grammar (TAG) for context sensitivity.

hgsvc. building variation graphs from hgsvc data

ultrabubble_eval. Extract detailed ultra bubble stats from a vg graph

spr. Compute the exact Subtree Prune and Regraft (SPR) distance between pair of unrooted phylogenetic trees

sg2vg. Prototype code for importing a Side Graph (from a GA4GH server) into a VG

cactus2hal. Convert progressive cactus database into a hal file

rgfa. keep track of some scripts used to evaluate rgfa stuff

sv-genotyping-paper. Shell

contigSim. Simulate the evolution of a genome as represented by a pool of contigs

cactus. Official home of genome aligner based upon notion of Cactus graphs

hal2sg. Prototype code for converting HAL to Sequence/String/Side/? Graph

snpBridge. Merge adjacent snps in a variant graph constructed from vcf, using genotype information in said vcf.