I used metaMDBG to assemble a metagenome. I checked quality of contigs with checkM to extract single contig HQ-MAGs.
Although most of single-contig HQ-MAG are fine, I found some of HQ-MAG that did not have clear Ori and Ter site with GC skew.
I would like to look into those unclear contigs with their raw reads (the reads were used to assemble the contigs).
Is there any way to find/extract all the reads that used to build a certain contigs using metaMDBG?
I used metaMDBG to assemble a metagenome. I checked quality of contigs with checkM to extract single contig HQ-MAGs. Although most of single-contig HQ-MAG are fine, I found some of HQ-MAG that did not have clear Ori and Ter site with GC skew.
I would like to look into those unclear contigs with their raw reads (the reads were used to assemble the contigs). Is there any way to find/extract all the reads that used to build a certain contigs using metaMDBG?