Pinned Repositories
HPRCyear1v2genbank
building a human pangenome from the HPRCy1v2 genbank accessioned assemblies
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
pgge
the pangenome graph evaluator
pgvf-spec
Pangenome Graph Variation Format (PGVF)
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/privacy-pangenomics
pangenome/odgi-paper
ODGI: understanding pangenome graphs (https://doi.org/10.1093/bioinformatics/btac308)
pangenome/WFA
Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
pangenome/chm13-grch38-liftover
liftover from the CHM13 T2T assembly to GRCh38 using wfmash
pangenome/resolve-nested-genotypes
pangenome/rs-gfa
GFA parser in Rust
pangenome/gfaestus
GFA visualizer, GPU-accelerated using Vulkan
pangenome/rs-gfa-utils
pangenome/saboten
pangenome/gbwt-wrapper
Exposes C api for the gbwt library
pangenome/rs-handlegraph
Rust implementation of VG handle graph
pangenome/gavlooth.github.io
Privacy pangenomics web page
pangenome/private-graphs-website
Privacy preserving graphs for pangenomics
pangenome/gfa-wrapper
Wrapper aroung rs-gfa that exposes C api
pangenome/abPOA
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
pangenome/Bandage
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
pangenome/odgi.github.io
ODGI suite documentation (Optimized Dynamic Genome/Graph Implementation)
pangenome/ssfog
scale-space filtering on genome graphs
pangenome/HPRCy1v2
pangenome build for human pangenome project year 1 genomes (version 2 assemblies)
pangenome/paf2dot
use gnuplot to generate a dotplot from sequence alignments in PAF format
pangenome/pgge
the pangenome graph evaluator
pangenome/burng
Removing complex regions from pangenome graphs
pangenome/HPRCy1
pangenome build for HPRC year 1 samples
pangenome/MHC
exploring the MHC in the HPRC year 1 samples
pangenome/rs-wfa
Rust bindings to the wavefront algorithm C implementation
pangenome/Computational-PANGenomics-2020
Online Training Course on the use of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types.
pangenome/CPANG20
computational pangenomics course 2020 edition
pangenome/pgvf-spec
Pangenome Graph Variation Format (PGVF)
pangenome/maffer
extract MSAs from genome variation graphs