- Module: An major component of MIDAS2, including Species, SNVs, CNVs and MIDASDB building.
- Analysis: Either the single-sample alignment-based tallying of reads mapped to SCGs (species), a representative genome (SNVs), or genes in a pangenome (CNVs) depending on which module is run OR the merging, filtering, and summarization of these results across samples.
- Workflow: The overall conceptual order of events from an implicit database and pre-requisite shotgun metagenomic samples through species selection and SNPs/genes modules, to results that will go into some sort of downstream analysis.
- Reference database: The upstream UHGG, GTDB, something user supplies, etc. that is then pre-processed to make a specific...
- MIDASDB: The pre-processed reference data in a format to be consumed by the MIDAS2 modules, including marker genes, reference genomes, pangenomes, etc.
- genome Index: Rather than bowtie2 database or some other ambiguous term
- Species-level pangenome: refers to the set of non-redundant genes (centroids) clustered from all the genomes within one species cluster.