kindel

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Does Kindel consensus consider base qualities?

1

Thank you for providing this useful tool to the community. I was wondering if base quality is considered when determining min-depth for the consensus call such as iVar ([https://andersen-lab.github.io/ivar/html/manualpage.html#autotoc_md19](https://andersen-lab.github.io/ivar/html/manualpage.html#autotoc_md19))?

sureman

bede

bede

bede

bede

Wrapper for easy reference guided contiguation + consensus of assemblies

2

Depend on aligner? Segemehl, BBMap? Graphmap?

bede

Test plotting

1

Maybe just replace with bokeh?

bede

Handle missing LN fields in @SQ headers

1

Accept reference as an optional argument and use to calculate length in absense of `LN` field Throw exception with missing LN field and no reference

bede

Function should return instance of `Consensus` object etc.

bede

Replace N's with the reference

3

Hi, For very bad alignments with a lot of gaps, is it possible to fill them using the reference instead N's? Thanks!

migrau