Metagenomic assemblies

Sample reads were co-assembled based on each sampling location using metaSPAdes v 3.11.1 with the following flags ‘-meta -t 16 --phred-offset 33 -m 500 -k 21,33,55,77,99,119’ and further filtered to a minimum scaffold length of 500 bp. Reads from samples and controls (i.e., extraction blank, filter blank, DI water blank) were mapped to co-assemblies using BWA-MEM. An approach similar to Dai et al.(Dai et al., 2020) was used to remove potential contaminant scaffolds.