Data Processing:
Metagenome reads were trimmed using Trimmomatic, and assembled into contigs with MEGAHIT. Reads were then mapped back to the contigs with Bowtie2 and SAMtools. Metagenome-assembled genomes were binned using MetaBAT, followed by curation of key genomes using Emergent Self Organizing Maps.
Software:
Trimmomatic v.0.36: Trimming software for read processing.
MEGAHIT v.1.1.1-2-g02102e1: Assembly software used to generate contigs from reads.
Bowtie2 v.2.2.9 and SAMtools v.1.3.1: Software used to map reads back to contigs and parse results of the mapping.
MetaBAT v.0.32.4: Binning software, used to group contigs into metagenome-assembled genomes (MAGs).
Emergent Self Organizing Maps (ESOM): manual binning software used to curate genomes of interest.
BCO-DMO Processing:
- removed commas from Collection_location column;
- removed directional letters from the Latitude and Longitude columns and made Latitude values negative to indicate South;
- converted Collection_date field to YYYY-MM format.