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nanopolish addition beside medaka #87

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replikation opened this issue Mar 24, 2021 · 1 comment

Owner

replikation commented Mar 24, 2021

implement the nanopolish option also if fast5 was provided as input?

Collaborator

hoelzer commented Mar 24, 2021

I think that would be really interesting, also to compare the final consensuses.

We then just need to be aware of some slight differences in the processing of the files as described here:
https://artic.readthedocs.io/en/latest/minion/

See "Variant calling"

Note: we use the $SAMPLE.trimmed.rg.sorted.bam alignment for the nanopolish workflow as nanopolish requires some leading sequence to make variant calls; we use the primer sequence for this purpose in order to call variants at the start of amplicons.

With medaka, the $SAMPLE.primertrimmed.rg.sorted.bam is used instead!

replikation mentioned this issue

Nanopolish implement #90

Merged

replikation closed this as completed

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