hi ,
I am doing a whole genome sequencing of a fungi of size ~20 mb. I have done a 500 bp library paired end 2*75 bp illumina miseq sequencing with 50x coverage. But several genes (~8% core genes) are remained uncovered. It is not an assembly issue. I have checked several short fragments of the genes in the raw fastq file and they are absent.Now what should I do to cover the maximum genes? Will a mate pair library with larger inserts help? or sequencing with ion torrent with its larger product size would be a better option?
I am doing a whole genome sequencing of a fungi of size ~20 mb. I have done a 500 bp library paired end 2*75 bp illumina miseq sequencing with 50x coverage. But several genes (~8% core genes) are remained uncovered. It is not an assembly issue. I have checked several short fragments of the genes in the raw fastq file and they are absent.Now what should I do to cover the maximum genes? Will a mate pair library with larger inserts help? or sequencing with ion torrent with its larger product size would be a better option?
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