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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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HERRO corrected ONT with trio data #2332

Closed YouxinZhao closed 3 months ago

YouxinZhao commented 3 months ago

I have the HERRO corrected ONT data (Basecalling Dorado v5 Sup) and the trio data.

canu -trim-assemble -p asm1 -d name genomeSize=2600m -nanopore-corrected corrected.fasta -haplotypeG25 GX_25small.fq.gz -haplotypeG9 /GX_9.fq.gz

Q1: Should i use -trim-assemble or -assemble Q2: Should i use -nanopore-corrected or HiFi ?

skoren commented 3 months ago

You should treat HERO data as HiFi and to use it with trio, it requires the same workaround as HiFi data documented here: https://canu.readthedocs.io/en/latest/quick-start.html?highlight=trio#trio-binning-assembly. However, I'd strongly recommend using a more recent assembler from the combination of HERRO+uncorrected ONT data like verkko, hifiasm, or LJA (if you have a homozygous genome).