PacBio internal control showing up in polished HGAP assembly

[jbadalam]

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.

[rhall]

The internal control is not removed in the HGAP process, the expectation is that it results in a single contig for the control.

[jbadalam]

Makes sense. Thanks for the rapid reply!