I am working on a de novo sequencing project of a yeast of size ~20 mb. I have done a 500 bp library paired end 2*150 bp illumina miseq sequencing with 50x coverage.But several portions of the genome are missing. Now I am planning to do pacbio long read sequencing 2 SMRT cells for the missing regions. My question is if I use pacbiotoca for assembly, will the long reads which contain the missing regions be filtered out because there is no short reads to correct them?
Can you suggest any alternate strategy? Assembly only with Pacbio reads is an option,but I think it requires a very high coverage of ~100x which is out of my budget.
Can you suggest any alternate strategy? Assembly only with Pacbio reads is an option,but I think it requires a very high coverage of ~100x which is out of my budget.
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