Quality filtering of reads with more than K bases under quality score

Question

[Rezenman]

Hey all, I am currently working on an analysis of barcode sequencing and looking for a tool to filter reads with K bases under a specific quality score. Does anyone have an idea of such a tool ? Thanks ahead

Answer 1

[ATpoint]

Skewer https://github.com/relipmoc/skewer has an option to filter for a minumum average quality:

-Q, --mean-quality <int> The lowest mean quality value allowed before trimming; (0)

Since the barcodes are probably of equal length it should not be difficult to calculate an average minumum score based on your requirements to be used with this option.