microcosM¶
Optimised, Comprehensive Metagenomics
microcosM is a modular, robust pipeline for streamlining complex metagenomic data analysis workflows.
microcosM provides solutions to both rapid, read-level taxonomic classification and high-resolution genome assembly. With a modular design and a rich suite of updated, carefully curated tools, data analysis workflows can be easily customised in a trackable manner to meet diverse research questions and resource settings.
Key Features¶
Read-based Analysis¶
Taxonomic assignment for each sequencing read is performed using an optimized combination of sourmash and YACHT. This approach ensures fast, scalable processing, even for large datasets. Reference databases can be customized to fit your specific research needs.
Detection of antimicrobial resistance genes (ARGs) is integrated via rgi_bwt, providing actionable insights into resistance profiles.
Metagenome Assembly & Binning¶
The pipeline assembles contigs and performs binning to recover Metagenome Assembled Genomes (MAGs), enabling in silico characterization of microbial communities.