stajichlab/AAFTF

[Enhancement] Assembly for Nanopore reads

Opened this issue · 2 comments

llk578496 commented

Hi! We have sequenced some isolates of Candida auris and would like to perform de novo assembly. May we ask is it possible to add support for Nanopore reads?

hyphaltip commented

I'll get around to this but generally the long read assembly ecosystem is pretty easy to run -- I would just run regular assemblers for now (canu, flye, masurca, necat) and test their performance. Once you have an assembly you can run medaka on the nanopore assembly with nanopore reads, if you have illumina data you can follow with pilon if you like. other steps like sourpurge will work and can still be run with AAFTF.

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llk578496 commented

Thanks a lot!