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@pangenome

pangenome

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2.8 %

pggb

the pangenome graph builder

odgi

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs

smoothxg

linearize and simplify variation graphs using blocked partial order alignment

impg

implicit pangenome graph

maffer

extract MSAs from genome variation graphs

PanSN-spec

Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes

vcfbub

use variant nesting information to flter overlapping sites from vg deconstruct output

pgge

the pangenome graph evaluator

pgvf-spec

Pangenome Graph Variation Format (PGVF)

HPRCyear1v2genbank

building a human pangenome from the HPRCy1v2 genbank accessioned assemblies

pggb-workshop

tutorial on pggb

spodgi

RDF and SPARQL ideas to build on top of [odgi](https://github.com/pangenome/odgi)

pggb-paper

The PanGenome Graph Builder

gfagino

your friendly pangenome graph genotyper

pangenome.github.io

jbrowse-visualization

Workflow to visualize pggb graphs in jbrowse

MemPanG23

Computational Pangenomics in Memphis

gfa-wp

Convert GFA W-lines to P-lines

resolve-nested-genotypes

chm13-grch38-liftover

liftover from the CHM13 T2T assembly to GRCh38 using wfmash

lifetree

hard mode all genomes alignment

chromosome_communities

Recombination between heterologous human acrocentric chromosomes

HPRCy1

pangenome build for HPRC year 1 samples

ssfog

scale-space filtering on genome graphs

rs-peanut

GAF alignment evaluation tool.

mafchunk

split MAF blocks into smaller chunks

sorting-paper

Path-Guided Stochastic Gradient Descent layout of pangenome graphs

MHC

exploring the MHC in the HPRC year 1 samples

phage-evo-paper

Repository to store the analysis of the paper on phage evolution.

seqwish-paper

Unbiased pangenome graphs

gfalace

lace up GFA files using panSN path name sub-ranges to coordinate the lacing

domibubble

sketch of bubble detection via dominator trees

privacy-pangenomics

HumanPangenomeBYOD2024

Material for the Human Pangenome Bring Your Own Data (BYOD) analysis Workshop 2024, October 21-25 in Cape Town, South Africa.

paf2dot

use gnuplot to generate a dotplot from sequence alignments in PAF format

odgi-paper

ODGI: understanding pangenome graphs (https://doi.org/10.1093/bioinformatics/btac308)

burng

Removing complex regions from pangenome graphs

odgi.github.io

ODGI suite documentation (Optimized Dynamic Genome/Graph Implementation)

keane_mouse_pangenome

HPRCy1v2

pangenome build for human pangenome project year 1 genomes (version 2 assemblies)

private-graphs-website

Privacy preserving graphs for pangenomics

flubble

finding single-entry single-exit bubbles in the flowgraph