pangenome

graphical pangenomic methods

Pinned Repositories

HPRCyear1v2genbank
building a human pangenome from the HPRCy1v2 genbank accessioned assemblies
Language:Shell12 4 10
impg
implicit pangenome graph
Language:Rust29 5 95
maffer
extract MSAs from genome variation graphs
Language:C++32 4 41
odgi
Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
Language:C++184 14 13638
PanSN-spec
Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
28 4 31
pggb
the pangenome graph builder
Language:Shell341 13 16138
pgge
the pangenome graph evaluator
Language:Shell21 5 82
pgvf-spec
Pangenome Graph Variation Format (PGVF)
18 3 00
smoothxg
linearize and simplify variation graphs using blocked partial order alignment
Language:C++56 6 316
vcfbub
use variant nesting information to flter overlapping sites from vg deconstruct output
Language:Rust22 5 51

pangenome's Repositories

pangenome/pggb
the pangenome graph builder
Language:Shell341 13 16138
pangenome/odgi
Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
Language:C++184 14 13638
pangenome/smoothxg
linearize and simplify variation graphs using blocked partial order alignment
Language:C++56 6 316
pangenome/impg
implicit pangenome graph
Language:Rust29 5 95
pangenome/PanSN-spec
Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
28 4 31
pangenome/vcfbub
use variant nesting information to flter overlapping sites from vg deconstruct output
Language:Rust22 5 51
pangenome/HPRCyear1v2genbank
building a human pangenome from the HPRCy1v2 genbank accessioned assemblies
Language:Shell12 4 10
pangenome/pggb-workshop
tutorial on pggb
11 3 12
pangenome/spodgi
RDF and SPARQL ideas to build on top of [odgi](https://github.com/pangenome/odgi)
Language:Python11 5 144
pangenome/gfagino
your friendly pangenome graph genotyper
Language:Rust10 4 00
pangenome/pangenome.github.io
Language:HTML9 4 02
pangenome/pggb-paper
The PanGenome Graph Builder
Language:TeX9 8 11
pangenome/povu
Language:C++8 3 11
pangenome/gfa-wp
Convert GFA W-lines to P-lines
Language:Rust7 5 0
pangenome/jbrowse-visualization
Workflow to visualize pggb graphs in jbrowse
Language:Shell71
pangenome/MemPanG23
Computational Pangenomics in Memphis
Language:HTML7 7 02
pangenome/chromosome_communities
Recombination between heterologous human acrocentric chromosomes
Language:R5 4 0
pangenome/lifetree
hard mode all genomes alignment
Language:Shell5 3 02
pangenome/mafchunk
split MAF blocks into smaller chunks
Language:Rust4 3 0
pangenome/rs-peanut
GAF alignment evaluation tool.
Language:Rust4 3 10
pangenome/gfalace
lace up GFA files using panSN path name sub-ranges to coordinate the lacing
Language:Rust3 3 0
pangenome/phage-evo-paper
Repository to store the analysis of the paper on phage evolution.
Language:Python3 3 0
pangenome/seqwish-paper
Unbiased pangenome graphs
Language:TeX3 3 0
pangenome/sorting-paper
Path-Guided Stochastic Gradient Descent layout of pangenome graphs
Language:TeX3 6 02
pangenome/MemPanG24
Computational Pangenomics in Memphis
Language:HTML2 1 01
pangenome/flubble
finding single-entry single-exit bubbles in the flowgraph
Language:Rust1 3 0
pangenome/keane_mouse_pangenome
Language:R1
pangenome/MemPanG25
Computational Pangenomics in Memphis
Language:HTML
pangenome/privvg
Differential privacy for graphs
3 0
pangenome/tree_of_life_alignment
Language:Shell3 0