use of purge haplotigs with falcon-phase

[Juke34]

Here a resume of the size of my genome after each step

assembly	primary size (bp)	haplotig size (bp)	total (bp)
falcon unzip	879494072	161125037	1040619109
falcon unzip post purge Haplotigs	615743546	420594391	1036337937
falcon phase round1	679010065	280054206	959064271
scaffolding with allHic	679064365	280054206	959118571
falcon phase round2	703831469	252736878	956568347

The first round of falcon phase sounds to re-incorporate within the primary assembly a part of what has been filtered out by purge haplotigs from the primary assembly.

Is it something expected? I just wondering if this result sounds normal or if I should try different parameters within falcon-phase.

[shawnpg]

Hi,

In general, yes, FALCON-Phase will move sequence from the haplotigs back into the primary contigs (and vice versa). What it is doing is looking at the Hi-C data to see if it can determine heterozygous sequences that likely originated from the same molecule in the nucleus. The long reads alone can often be insufficient information for correct phasing.

Thanks,

Shawn