So I've got a newly assembled genome that was sequenced using PacBio sequencing and obtained >100x coverage. It was assembled with HGAP.3 and for the most part looks great except for an exceptionally large contig (the largest actually). it's estimated that our genomes largest chromosome is around 3.5Mb (based on electrokaryograph) but this one large contig is around 5Mb and has low complexity across the entire contig. Blasting this contig doesn't result in any matches of note at NCBI or to our reference genome.
Any suggestions on how I could adjust the assembly to get rid of this large contig that I am fairly sure is not real?
Any suggestions on how I could adjust the assembly to get rid of this large contig that I am fairly sure is not real?
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