pailloufat-stack

It is a diploid sample yes. I do that assembly for another team, and they know some closed species which are around 1.2Gb and so, they expect that size for...

For both haplytopes, I have : ``` # number of contigs: 1045 # total contigs length: 1325235316 # mean contig size: 1268167.77 # contig size first quartile: 35642 # median...

I got my BUSCO results :  As you said, using purge_dups is too aggressive and reduce the contiguity of my primary assembly. Of course, the number of duplicated genes...

As you suggested to set `-s 0.45` , I tried it. I nearly got the same assembly metrics : ``` # number of contigs: 853 # total contigs length: 1440131087...

I agree, I should stay with the defaults v15 results. That's the BUSCO results on both haplotypes : 

I also used the v0.12 version of hifiasm , and I got these metrics on the primary assembly : ``` # number of contigs: 653 # total contigs length: 1333035279...

When I set up `--n-hap 3 ` with v0.15, I got : ``` # number of contigs: 828 # total contigs length: 1431860996 # mean contig size: 1729300.72 # contig...

@chhylp123 I'm gonna have a look on these duplicated genes, you're right! I will let you know. So, many of the duplicated genes (393) found by BUSCO are the same...

Thanks for your quick and complete feedback! I know `lima` first trims the barcodes, and can trim the primers in a second run with the primer sequences (https://lima.how/faq/primer.html) I guess...