Closed dcopetti closed 4 years ago
Hi Dario,
I wouldn't recommend to tweak those - otherwise it might cause chimeric connections from disjointigs propagated to the graph. What is the expected divergence rate? If is relatively high, Flye should be able to reconstruct the alternative alleles with the default paramteres. The assembly will be more fragmented though, since Flye currently does not do pseudo-haplotyping (as in Falcon).
I'd wait for assembly to complete and see how it looks. Coverage will definitely be helpful in identifying haploid/diploid contigs.
Mikhail
I'm closing the issue for now, but feel free to reopen if you have more questions about this assembly later!
Hi, I am assembling a heterozygous 2.5 Gb (haploid size, so we expect a ~5 Gb assembly) plant genome. We have about 35x coverage per allele and many copies of a very few repeats (LTR-retrotransposons). The assembly is ongoing now, but I wonder if for the next iterations I should/can tweak some of these parameters
to reduce the collapsing of repeats into one node and the collapsing of the two allelic sequences into one contig. Would you touch something, with the goal of being more selective when finding overlaps? Would the coverage be of any help to identify the two sets of allelic sequences in a pile of alignments? Thanks, Dario