I am finding that pilon will make orders of magnitude fewer changes on unzip assemblies. The median number of changes that pilon makes on alternate contigs is 0. This is despite running bwa in alt-aware mode. I did notice that most of the alignments had bit 0x800 set (supplemental) so I tried clearing this bit and still pilon made no changes to alternate contigs, despite having many reads aligned to those contigs.
Has anyone successfully used pilon on Falcon unzip assemblies, including on the alternate contigs?
I am finding that pilon will make orders of magnitude fewer changes on unzip assemblies. The median number of changes that pilon makes on alternate contigs is 0. This is despite running bwa in alt-aware mode. I did notice that most of the alignments had bit 0x800 set (supplemental) so I tried clearing this bit and still pilon made no changes to alternate contigs, despite having many reads aligned to those contigs.
Has anyone successfully used pilon on Falcon unzip assemblies, including on the alternate contigs?