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Support of minimap2, bam mem2 and bwa aln #181

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agalitsyna opened this issue Nov 8, 2022 · 1 comment

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agalitsyna commented Nov 8, 2022

Adding an opportunity to select the aligner out of:

minimap2 and single-end data distiller with an option to process with minimap2 #177
- requires mapping with parse2 instead of parse
bwa mem2 which is a fast optimized bwa mem
bwa aln optimized for single end https://github.com/open2c/distiller-nf/pull/171/files

Pros:

flexibility for multiple types of data
Cons:
reduced readability
more code and params

agalitsyna mentioned this issue

distiller 0.3.5 roadmap #182

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6 tasks

mxw010 commented Dec 2, 2022

if you were to add those mapper, would you consider adding chromap as well? In our experience it performs just as well and is significantly faster.

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