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rnajena / mycovista

Mycovista - M. bovis assembly pipeline
GNU General Public License v3.0
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POLCA polishing #13

Closed hoelzer closed 4 years ago

hoelzer commented 4 years ago

New tool: https://www.biorxiv.org/content/10.1101/2019.12.17.864991v1

tldr;

Idea: we could add a rule for POLCA and compare the outcome.

sandraTriebel commented 4 years ago

I didn't read the whole paper, but it look's nice.

But POLCA is part of the MaSuRCA genome assembly toolkit (https://github.com/alekseyzimin/masurca), which include an assembler too (we didn't include this assembler in the comparison in my bachelor thesis, because it would have been too much). So it's possible, that POLCA might work better with this assembler than flye, isn't it?

POLCA only uses short reads for polishing a long-read assembly, so it could replace the 4 Racon runs w/ SR (1). Or should we polish the flye assembly with POLCA (2)?

(1) flye -> 4x Racon w/ LR -> 1x medaka w/ LR -> POLCA w/ SR (and compare these results with the current pipeline) (2) flye -> POLCA w/ SR

hoelzer commented 4 years ago

Ah interesting that it is part of MaSuRCA.

As far as I understood POLCA is for polishing an assembly using short reads, so I would say:

(1) flye -> 4x Racon w/ LR -> 1x medaka w/ LR -> POLCA w/ SR (and compare these results with the current pipeline)

would be the way to go.

sandraTriebel commented 4 years ago

We leaved POLCA out of the pipeline, because it would require a precise evaluation of the results. Moreover, POLCA is considered to use within the MaSuRCA pipeline.