GaetanBenoitDev / metaMDBG

MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
MIT License
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Extracting raw reads for a contig #20

Open Sung-hub opened 2 days ago

Sung-hub commented 2 days ago

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?

GaetanBenoitDev commented 2 days ago

Not directly with metaMDBG. You can map back the reads to the contigs with minimap2.