Parameters for triploid HIFI

ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

GNU General Public License v3.0

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Parameters for triploid HIFI #239

Open ptranvan opened 2 years ago

ptranvan commented 2 years ago

Hi I am working on a triploid species which is highly heterozygous, see genomescope plot

http://qb.cshl.edu/genomescope/genomescope2.0/analysis.php?code=nnC4CPmgLE3605rbyM7y

My data is Hifi and I used -x ccs. I would like to know if you have other recommendations for parameters regarding my species ? thanks.

ruanjue commented 2 years ago

Try -x ccs first, if not good, try to increase -s from 0.5 to 0.7 or ?.

ptranvan commented 2 years ago

Do I need to polish the HIFI assembly with this ?

minimap2 -t16 -ax map-pb -r2k dbg.raw.fa reads.fa.gz | samtools sort -@4 >dbg.bam
samtools view -F0x900 dbg.bam | ./wtpoa-cns -t 16 -d dbg.raw.fa -i - -fo dbg.cns.fa

ruanjue commented 2 years ago

Yes, polish it