Pinned Repositories
gafpack
convert variation graph alignments to coverage maps over nodes
impg
implicit pangenome graph
maffer
extract MSAs from genome variation graphs
odgi
Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
PanSN-spec
Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
pggb
the pangenome graph builder
pggb-workshop
tutorial on pggb
pgge
the pangenome graph evaluator
smoothxg
linearize and simplify variation graphs using blocked partial order alignment
vcfbub
use variant nesting information to flter overlapping sites from vg deconstruct output
pangenome's Repositories
pangenome/pggb
the pangenome graph builder
pangenome/odgi
Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
pangenome/smoothxg
linearize and simplify variation graphs using blocked partial order alignment
pangenome/impg
implicit pangenome graph
pangenome/PanSN-spec
Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
pangenome/pggb-workshop
tutorial on pggb
pangenome/vcfbub
use variant nesting information to flter overlapping sites from vg deconstruct output
pangenome/gafpack
convert variation graph alignments to coverage maps over nodes
pangenome/HPRCyear1v2genbank
building a human pangenome from the HPRCy1v2 genbank accessioned assemblies
pangenome/pggb-paper
The PanGenome Graph Builder
pangenome/spodgi
RDF and SPARQL ideas to build on top of [odgi](https://github.com/pangenome/odgi)
pangenome/gfagino
your friendly pangenome graph genotyper
pangenome/povu
pangenome/jbrowse-visualization
Workflow to visualize pggb graphs in jbrowse
pangenome/pangenome.github.io
pangenome/HumanPangenomeBYOD2024
Material for the Human Pangenome Bring Your Own Data (BYOD) analysis Workshop 2024, October 21-25 in Cape Town, South Africa.
pangenome/MemPanG23
Computational Pangenomics in Memphis
pangenome/gfalace
lace up GFA files using panSN path name sub-ranges to coordinate the lacing
pangenome/chromosome_communities
Recombination between heterologous human acrocentric chromosomes
pangenome/genotypify
Genotyping lots of samples with big pangenomes
pangenome/lifetree
hard mode all genomes alignment
pangenome/mafchunk
split MAF blocks into smaller chunks
pangenome/rs-peanut
GAF alignment evaluation tool.
pangenome/seqwish-paper
Unbiased pangenome graphs
pangenome/sorting-paper
Path-Guided Stochastic Gradient Descent layout of pangenome graphs
pangenome/MemPanG24
Computational Pangenomics in Memphis
pangenome/flubble
finding single-entry single-exit bubbles in the flowgraph
pangenome/keane_mouse_pangenome
pangenome/MemPanG25
Computational Pangenomics in Memphis
pangenome/tree_of_life_alignment