Regarding the maximum length of contigs

[mdrishti]

Hi @zhixingfeng ,

I am using igda for detecting sublines of one bacteria in a pooled PacBio Sequel II genomic data. The average length of reads is 8kb. I find that igda gives me very few contigs (3-6) for most of datasets. I do not expect 100s of sublines, but I do expect at least 2-3. In my igda results, I get 6 contigs placed very very far apart from each other on a 5Mb genome. From variant analysis, I know that the loci covered by these contigs are either deleted or have a high frequency of mutation (~80%). Do you think that these results could be due to smaller length of reads, thus limiting the maximum achievable length of the contig by igda? Or is it that I am doing something wrong (I followed exactly the commands suggested on the usage page for Sequel II reads)? Any insights will be super useful.