I noticed something odd when running two different HGAP assemblies. In both cases, the polished_assembly.fasta files contained a ~4kb contig with >3000x coverage. It matches the sequence of PacBio's 3-10kb SMRTbell internal control, and when I run resequencing or base modification pipelines it shows the control spike data. I just can't figure out why it's showing up in the final assembly.
This doesn't appear to be a huge issue, since I can just remove the contig from the fasta file. Just wondering if anyone else has encountered this.
The pipeline I used was HGAP.2 in SMRTanalysis 2.1.0.
This doesn't appear to be a huge issue, since I can just remove the contig from the fasta file. Just wondering if anyone else has encountered this.
The pipeline I used was HGAP.2 in SMRTanalysis 2.1.0.
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