Question: how about polishing a phased diploid genome assembly?

[Yutang-ETH]

Question: how about polishing a phased diploid genome assembly?

[auryjm]

Hi Yutang,

Thank your for your kind message, it's always encouraging to see that our tools are useful !

• I would say yes, as polishing the diploid assembly will ensure better alignment of individual reads. However, in case you have an haploid assembly, Hapo-G will try to avoid phase switches (within the limit of read length and SNP frequency).
• Indeed, if most of the changes are homo it may indicate that your assembly is correctly phased. There are two ratios, one for the pile of alignment used for polishing (i.e. without reads that may correspond to the second haplotype) and one for the whole set of alignments.

Hope this helps,

Jean-Marc

[Yutang-ETH]

Hi Jean-Marc,

Thank you very much for your comments, they are very helpful, and I have to say this again, HAPO-G is really wonderful.

Cheers,
Yutang