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wslh-bio / SPNtypeID

SPNtypeID is a Nextflow pipeline used for genome assembly and serotyping of Streptococcus pneumoniae.
GNU General Public License v3.0
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Change PASS/FAIL thresholds for coverage from 70X to 40X #5

Closed AbigailShockey closed 1 year ago

AbigailShockey commented 1 year ago

Description of feature

Based on the results of the subsampling analysis, the coverage QC threshold should be changed from 70X to 40X

k-florek commented 1 year ago

I pushed all of the quality thresholds including minimum coverage, minimum average quality, and percentage SPN and Strep into the config file so these can all be adjusted within the config file.