Unsupported sequence in assembly

[jmdiesel16]

Hello,

While using hifiasm (0.16.1-r375), I've come across a strange issue. I have aligned the reads that were used to create the assembly back onto the assembled contigs, and have found a 24-bp insert in the assembly that is not present in any of the ccs reads that align to the region. In the screenshot below, the read highlighted in red is listed in the noseq.gfa file as being used for this particular region.

The 24-bp insert is supported by a few hi-c reads that align to this region. Is it possible that sequence from the hi-c reads got incorporated?

Any insight is much appreciated.

[chhylp123]

Hifiasm does not use HiC for consensus. This might be the issue of hifiasm during the error correction or consensus, or the alignment issues if the target region is very complex. If this region is not such complex, you can safely trust the alignment results.