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Replace nanofilt with filtlong to reduce the number of bad small reads #43

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Thomieh73 opened this issue Jul 10, 2023 · 6 comments
Open

Replace nanofilt with filtlong to reduce the number of bad small reads #43

Thomieh73 opened this issue Jul 10, 2023 · 6 comments
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This to implement a method that is more tuneable with respect to keeping the best reads in the dataset.
@Thomieh73 Thomieh73 added the enhancement New feature or request label Jul 10, 2023
@Thomieh73 Thomieh73 self-assigned this Jul 10, 2023
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Or should I replace it with Rasusa: https://github.com/mbhall88/rasusa

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

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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 Thomieh73 changed the title Replace nanofilt with filtlong Replace nanofilt with filtlong or Rasusa Sep 14, 2023
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Replace Nanofilt with Chopper.

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

@Thomieh73 Thomieh73 changed the title Replace nanofilt with filtlong or Rasusa Replace nanofilt with fChopper Mar 7, 2024
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https://github.com/wdecoster/chopper

@Thomieh73 Thomieh73 changed the title Replace nanofilt with fChopper Replace nanofilt with Chopper Mar 7, 2024
@Thomieh73 Thomieh73 changed the title Replace nanofilt with Chopper Replace nanofilt with filtlong to reduce the number of bad small reads Jan 29, 2025
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See also issue #36

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