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Glenn Hickey

Expert
@glennhickey

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

89

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

7

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

6

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

5

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

4

vg2sg. C++

3

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

3

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

2

hgsvc. building variation graphs from hgsvc data

2

ultrabubble_eval. Extract detailed ultra bubble stats from a vg graph

1

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

1

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

1

cactus2hal. Convert progressive cactus database into a hal file

1

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

1

sv-genotyping-paper. Shell

1

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

1

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

1

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

1

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

1