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NorwegianVeterinaryInstitute / Nepal

NExtflow Pipeline for AmpLicons
BSD 3-Clause "New" or "Revised" License
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Replace nanofilt with Chopper #43

Open Thomieh73 opened 1 year ago

Thomieh73 commented 1 year ago

This to implement a method that is more tuneable with respect to keeping the best reads in the dataset.

Thomieh73 commented 1 year ago

Or should I replace it with Rasusa: https://github.com/mbhall88/rasusa

Thomieh73 commented 1 year ago

https://joss.theoj.org/papers/10.21105/joss.03941

Thomieh73 commented 1 year ago

See also this paper https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000294

An alternative strategy deployed to reduce the computational burden of hybrid assembly was to randomly subsample long reads until a certain expected coverage was reached. [Table 1](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000294#T1) shows that this strategy was preferable to read correction and filtration: it did not reduce assembly completeness but did reduce computation time.
Thomieh73 commented 8 months ago

Replace Nanofilt with Chopper.

Filtlong and Rasusa should be used differently, since there goal is really to reduce the complexity of the dataset.

Thomieh73 commented 8 months ago

https://github.com/wdecoster/chopper