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apcamargo / genomad

geNomad: Identification of mobile genetic elements
https://portal.nersc.gov/genomad/
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Is it safe to run genomad directly on nanopore R10.4.1 long reads? #30

Open xinehc opened 10 months ago

xinehc commented 10 months ago

Hi,

Thanks for providing genomad, it is very useful.

I was wondering would it be OK to run genomad directly on raw nanopore reads (>1000 bp, median q19) instead of assembled contigs? Should the parameters be tuned in this case?

apcamargo commented 10 months ago

Ho @xinehc,

Yes, you can. One limitation is that indels could cause problems for the gene calling algorithm, but the extent of this depends on the chemistry and base calling algorithm you used.

Please let me know of your experience with it on the Nanopore reads!