Analysis code — Substrate-associated variation in Ramalina bacteriobiomes and identification of Mucilaginibacter licheni sp. nov. through genome-resolved metagenomics

Abstract

Analysis code for the metagenome assembly, bin refinement/QC, read mapping/coverage, taxonomic profiling, genome taxonomy/phylogenetics, genome annotation, and COG functional-annotation comparison steps described in the Materials and Methods of "Substrate-associated variation in Ramalina bacteriobiomes and identification of Mucilaginibacter licheni sp. nov. through genome-resolved metagenomics" (submitted to PLOS ONE, manuscript ID PONE-D-26-35785). Covers the metaSPAdes/MEGAHIT/IDBA-UD assembler comparison and the CONCOCT/MetaBAT2/MaxBin2 + DAS Tool binning and refinement pipeline for both R. polymorpha and R. sinensis, HPC batch scripts for QC (CheckM), read mapping and genome-level coverage (Bowtie2, CoverM), taxonomy-aware Prokka annotation, read-based taxonomic composition (Kaiju), GTDB-Tk/TYGS phylogenomic tree generation for the novel species RP MAG 010, and the COG-category functional comparison of RP MAG 010 against four reference Mucilaginibacter genomes (Figs 3–4). See the included README for full scope, pipeline order, and software requirements.