A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.
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Updated
Sep 24, 2019 - Python
A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.
Scripts for Hill et al. (in review) 🌾
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
Alignment of Pangenome Graphs with Ricci Flow
Advancing the Indian Cattle Pangenome: Characterizing Non-Reference Sequences in Bos indicus
Pangenomic Statistical analysis in R (pasaR)
bacterial metagenomes and pangenome graphs from both illumina and long reads
pangenome metagenomics normalizer for gene annotations specifically gene ontologies.
Optimal sequence-to-graph alignment with recombinations using wavefront algorithm.
Notes upon pangenome graphs construction
CPANG19 - Computational PANGenomics (2019)
This repository contains the files from my master thesis project required to conduct a whole-genome analysis of haploblocks in wheat based on pairwise comparisons between assemblies. This is based on a previous method (https://doi.org/10.1038/s42003-020-01413-2), but focuses on the the quality of the pairwise comparisons to call haplotypes.
Functions for working with NCBI's Pathogen Detection data
Repository dedicated to the experiment section of the paper: Revisiting pangenome openness with k-mers. PCJ Math & Comp Biol. (2024).
PAPi (Pangenome Analysis Pipeline)
The lumpy skin disease virus (LSDV) pangenome variation graph (PVG)
Analysis of shared parts of a pangenome
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.
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