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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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N50 < 10000 #135

Closed MarcelaHer closed 2 years ago

MarcelaHer commented 2 years ago

Hi, is there any option to run this program with N50<10000? Thanks

apetkau commented 2 years ago

Hello @MarcelaHer

You can adjust the minimum N50 value with --minimum-N50-value:

  --minimum-N50-value MINIMUM_N50_VALUE
                        The minimum N50 value for the quality metrics. Defaults to 10000. [10000].

However, all this does is changes the quality module status from Fail to Pass. The N50 value and minimum/maximum length values for a genome just change that status, they don't have any other effect on the output.