#4 · Systems biology

Updated tools for microbial pangenomics, plasmid recovery and phylogenetic inference

The dominant thread is the engineering of analysis tools for microbial and metagenomic genomics, with emphasis on scalability, modularity and resolution. PPanGGOLiN V2 extends a graph-based statistical pangenome tool with a redesigned architecture and faster performance on large datasets. PlasChain builds on SCAPP's cycle-peeling by adding contig paths and cycle merging to recover long plasmids from short-read metagenome assemblies. A parallelized balanced minimum evolution algorithm replaces recursion with flattened arrays and reports a multi-dozen-fold speedup over FastME. BIP and MeioBIOME package end-to-end workflows, containerized and Snakemake-based respectively. The cumulative cgMLST study is distinct in scope, adding nested core-loci sets that raise pairwise allelic distances 5.6-fold for Klebsiella pneumoniae typing. What is new is the combination of workflow packaging with algorithmic speed and finer-grained discrimination.