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39 public repositories
matching this topic...
This repo contains scripts used for the identification of phylogenetic marker genes (PMGs) in assembled metagenomic data. Code is provided for benchmarking this method on sequenced genomes as well as running this analysis on metagenomic data. These scripts are in development.
Updated
Jul 27, 2018
Python
A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.
Updated
Sep 24, 2019
Python
A Snakemake workflow for microbial pangenomics analyses.
Updated
Jun 29, 2023
Perl
Repository dedicated to the experiment section of the paper: Revisiting pangenome openness with k-mers. bioRxiv. (2023).
Updated
May 27, 2024
Python
Optimal sequence-to-graph alignment with recombinations using wavefront algorithm.
Updated
Jul 28, 2023
Rust
Compare pangenomes using ED-Strings
pangenome metagenomics normalizer for gene annotations specifically gene ontologies.
Updated
May 2, 2024
Python
Introduction to the Command Line for Pangenomics
Updated
May 27, 2024
Python
PAPi (Pangenome Analysis Pipeline)
The lumpy skin disease virus (LSDV) pangenome variation graph (PVG)
Analysis of shared parts of a pangenome
Updated
May 24, 2024
Python
Topological data analysis for Comparative Genomics
Updated
May 27, 2024
Python
CPANG19 - Computational PANGenomics (2019)
Updated
Mar 26, 2020
Python
Pangenomics Workshop Overview
Updated
Apr 13, 2024
Python
Advancing the Indian Cattle Pangenome: Characterizing Non-Reference Sequences in Bos indicus
Notes upon pangenome graphs construction
Updated
Feb 22, 2024
TypeScript
bacterial metagenomes and pangenome graphs from both illumina and long reads
Updated
May 2, 2024
Shell
Scripts for Hill et al. (in review) 🌾
Library to parse, edit and handle in memory GFA graphs
Updated
May 16, 2024
Python
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