Description
Hi,
I would just like to make a return on the scaffolding of my assembly (Sanger technology) with PacBio reads (30x coverage), by using pyScaf.
pyScaf is fast and generates interesting results in the first place. I went from 2,059 scaffolds to 1,344 scaffolds, which was encouraging. Then I launched BUSCO on both assemblies and got the following results :
95.6% of complete BUSCO genes for my assembly (before pyScaf) and 78.7% of complete BUSCO genes after pyScaf. Before scaffolding, I have 37 missing genes, after pyScaf I have 284 missing genes.
I launched pyScaf with these parameters :
pyScaf.py -f Scaffolds.fasta --identity 0.80 -o Scaffolds.pyScaf.fasta -t 10 --log pyScaf_run.log --longreads all_raw_reads.Pacbio.fasta
Maybe I have to change them ? Do you have any advice to me?