Build a partitioned pangenome graph from microbial genomes

PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples

Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions

Integrate multiple genome assemblies into a pangenome graph

Strain-level abundances estimation in metagenomic samples using variation graphs

A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses

Non-redundant pangenome assemblies from multiple genomes or bins

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).

Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)

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.

Merge structural variations (SV) for pangenome VCF

Integrate multiple assemblies into a pangenome graph

Analysis of shared parts of a pangenome

A pipeline for pangenome wide association studies (panGWAS).

Extract flexible bacterial core genome alignments and compute SNP distances. Additionally, perform rarefaction-sampling analysis of alignments

Library to parse, edit and handle in memory GFA graphs

Sequence2Branches: Creating a species-level phylogenetic tree from paired FASTQ reads

Scripts to analyze the data for the paper "An outstanding bacterial membranome requires CRISPR-Cas systems to avoid the intervention of phages" and derive the figures or subfigures shown in the manuscript.

A repository as a Supplementary Methods of Moulana et al., 2019

Sensitive Alignments from a RYmer Index