pangenome
There are 66 repositories under pangenome topic.
labgem/PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
lh3/pangene
Constructing a pangenome gene graph
eead-csic-compbio/get_homologues
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
neherlab/pangraph
A bioinformatic toolkit to align genome assemblies into pangenome graphs
marschall-lab/panacus
Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
nf-core/pangenome
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
SegataLab/panphlan
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
SouthGreenPlatform/panache
Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.
at-cg/PanAligner
Long read aligner for cyclic and acyclic pangenome graphs
AnimalGenomicsETH/bovine-graphs
Integrate multiple genome assemblies into a pangenome graph
dubssieg/pancat
Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
iferres/pagoo
A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.
songtaogui/pan-Zea_construct
Workflow to construct linear representation of pan genome from deep WGS data and public assemblies
kevsilva/StrainFLAIR
Strain-level abundances estimation in metagenomic samples using variation graphs
songtaogui/panz-SV-pipe
Structure variants calling and genotyping scripts for pan-Zea
chmccarthy/Pangloss
Pangenome analysis of eukaryotes.
maxgmarin/panqc
A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses
songtaogui/pan-Zea_utilities
the miscellaneous analysis scripts used in the research of pan-Zea genome and genetics
fpusan/SuperPang
Non-redundant pangenome assemblies from multiple genomes or bins
qwx9/strangepg
strange pangenome and large graph visualization
444thLiao/pangenome_workflow
luigi based workflow for analysising WGS samples collecting from different source. It will auto clustering, annotating gene or species, and finally perform pangenome analysis(roary).
rx32940/BactPrep
Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)
gaojunxuan/chrom_mini_graph
Space-efficient minimizer-based pangenome reference graph and haplotype mapping tool
kloetzl/pangenomesim
♥ Simulate bacterial pangenomes.
pangenome/chromosome_communities
Recombination between heterologous human acrocentric chromosomes
iferres/simurg
Simulate pangenomes according to the IMG + Neutral models
salvadorlab/mbovpan
Mbovpan is a nextflow bioinformatic pipeline for Mycobacterium bovis pangenome analysis. The goal of Mbovpan is to help researchers to study the M. bovis pangenome in an automatic and easy way.
danangcrysnanto/bovine_pangenome_graph
Integrate multiple assemblies into a pangenome graph
FarhanaRiaz123/Pangenome-Analysis
Pangenome-Analysis.py is written for extraction of core, accessory and unique genomes (Gene families and proteins) along with filtration of single copy orthologues, creation of binary and count matrices as well as removal of duplicates.
dubssieg/gfagraphs
Library to parse, edit and handle in memory GFA graphs
dubssieg/sharepg
Analysis of shared parts of a pangenome
gi-bielefeld/pangrowth
Pangenome openness from k-mers
moorembioinfo/FlexCore
Extract flexible bacterial core genome alignments and compute SNP distances. Additionally, perform rarefaction-sampling analysis of alignments
ouzounis/my-figshare-pointers
datasets shared on figshare
SioStef/panplots
A small R script for generating pangenome accumulation curves
dubssieg/rs-pancat-compare
RUST port of pancat compare tool