Hi all,
I'm doing a denovo assembly of a cyanobacterial genome with SPades, all is working well but when there are multiple copies of a gene (e.g. 16srRNA gene), it appears that all reads associated with that gene are being mapped to a single contig.
Coverage of these contigs appears to correspond quite well to number of expected copies in the genome (i.e. normal coverage ~50x, for a contig with a gene with four copies, coverage ~200x).
Does anyone know of a method to prevent this from happening so that each of the copies assemble separately in different contigs?
Cheers
N
I'm doing a denovo assembly of a cyanobacterial genome with SPades, all is working well but when there are multiple copies of a gene (e.g. 16srRNA gene), it appears that all reads associated with that gene are being mapped to a single contig.
Coverage of these contigs appears to correspond quite well to number of expected copies in the genome (i.e. normal coverage ~50x, for a contig with a gene with four copies, coverage ~200x).
Does anyone know of a method to prevent this from happening so that each of the copies assemble separately in different contigs?
Cheers
N
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