Hi,
I'm trying to extend my contigs to cover entire viral genomes. When I align my reads (1.5M) to a viral genome (2.6KB), I can get full coverage of it and export a concensus sequence. When I assemble these reads, I get 2 contigs that cover about half of the viral reference sequence. I can scaffold (scaffold_builder: http://edwards.sdsu.edu/scaffold_builder/) these contigs, but I am missing two large sequences in the beginning and middle of the sequence (brackets denote missing sequence):
I know that my reads cover this sequence, but I think that they didn't make it into any contigs so the scaffold program can't use them to fill in the gaps.
My plan is to do the following: combine the reads that map to the reference with the contigs and use the scaffold builder on the contigs and reads together to fill in the gaps. This pipeline is running now, but I wanted to see if anyone has any other ideas about what to do?
Thanks!
I'm trying to extend my contigs to cover entire viral genomes. When I align my reads (1.5M) to a viral genome (2.6KB), I can get full coverage of it and export a concensus sequence. When I assemble these reads, I get 2 contigs that cover about half of the viral reference sequence. I can scaffold (scaffold_builder: http://edwards.sdsu.edu/scaffold_builder/) these contigs, but I am missing two large sequences in the beginning and middle of the sequence (brackets denote missing sequence):
Code:
reference: ----------------------------------- contigs: [ ]--------------[ ]-------
My plan is to do the following: combine the reads that map to the reference with the contigs and use the scaffold builder on the contigs and reads together to fill in the gaps. This pipeline is running now, but I wanted to see if anyone has any other ideas about what to do?
Thanks!
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