pangenomics
There are 42 repositories under pangenomics topic.
merenlab/anvio
An analysis and visualization platform for 'omics data
marschall-lab/panacus
Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
legumeinfo/gcv
Federating genomes with love (and synteny derived from functional annotations)
cucapra/pollen
generating hardware accelerators for pangenomic graph queries
marschall-lab/GFAffix
GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
algbio/GraphChainer
An accurate aligner of long reads to a variation graph, based on co-linear chaining
dubssieg/pancat
Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
at-cg/minichain
Long-read aligner to pangenome graphs
AlgoLab/RecGraph
Optimal sequence-to-graph alignment with recombinations
beiko-lab/arete
AMR/VF LGT focused bacterial genomics analysis workflow
noecochetel/North_American_Vitis_Pangenome
Construct and Analyze the North American Vitis pangenome
vinuesa/TIB-filoinfo
Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
peng-ye/MetaPGN
A pipeline for construction and graphical visualization of annotated pangenome networks.
carpentries-incubator/pangenomics
Pangenome Analysis in Prokaryotes Lesson
TurakhiaLab/panman
Pangenome Mutation-Annotated Networks
faylward/pangenomics
Scripts and utilities for pangenomic/phylogenomic analysis of prokaryotic genomes. Scripts for the analysis of genomic features such as C-ARSC, N-ARSC, and intergenic spacer lengths are also included.
dubssieg/rs-pancat-compare
Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.
darcyabjones/mumflow
A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.
dubssieg/sharepg
Analysis of shared parts of a pangenome
jamonterotena/Haplotype-based-Pangenome-Wheat-Analysis
Extension to the Crop Haplotypes website showing shared haplotypes between wheat genome assemblies. Enables mapping genomic regions of interest to the assemblies and calculate quality parameters such as alignment density or continuity
Rowena-h/GaeumannomycesGenomics
Scripts for Hill et al. (in review) 🌾
ampatzia/pasaR
Pangenomic Statistical analysis in R (pasaR)
carpentries-incubator/pangenomics-workshop
Pangenomics Workshop Overview
carpentries-incubator/topological-data-analysis
Topological data analysis for Comparative Genomics
emmaewade/pangenome-workflow
A Snakemake workflow for microbial pangenomics analyses.
Jtrachsel/pdtools
Functions for working with NCBI's Pathogen Detection data
dubssieg/gfagraphs
Library to parse, edit and handle in memory GFA graphs
dubssieg/pangenome-notes
Notes upon pangenome graphs construction
GCBL-NIAB/Bos_indicus_pangenome_10X
Advancing the Indian Cattle Pangenome: Characterizing Non-Reference Sequences in Bos indicus
jorgeavilacartes/panricci
Alignment of Pangenome Graphs with Ricci Flow
lucaparmigiani/Pangenome-Openness
Repository dedicated to the experiment section of the paper: Revisiting pangenome openness with k-mers. PCJ Math & Comp Biol. (2024).
carpentries-incubator/pangenomics-python
Introduction to Python: Pangenomics
chosenobih/rice_pangenomics
Scripts for de-novo genome assembly, assembly polishing, QC and post-assemble analyses of HiFi whole genome sequence data and downstream pangenomics analyses to identify structural variants
iFoxz17/WF_Recgraph
Optimal sequence-to-graph alignment with recombinations using wavefront algorithm.
biosustain/pankb_llm
An LLM-based pangenomics chatbot integrated into the PanKB website.