1. Contigs/Scaffolds with low read coverage

By default, MetaBAT will ignore low read coverage contigs/scaffolds determined after the abundance matrix is created. These contigs/scaffolds may arise from one of three reasons: 1) MetaBAT sets a higher mapping quality filtering threshold, which may decrease the actual read coverage as many mapped reads get filtered out, 2) some species may be present in many samples at low abundance, their genomes can still be assembled in the co-assembly protocol, or 3) they may represent fraudulent ones.

MetaBAT offers two options to control the read coverage filtering step. A per-sample threshold (--minCV) to control the minimum read coverage required (default 0.2x) in any sample and a total read coverage threshold (--minCVSum, default 1x) to control the minimum required read coverage in all samples combined.