Quality filtering of reads with more than K bases under quality score
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4.3 years ago
Rezenman • 0

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

sequencing next-gen • 520 views
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4.3 years ago
ATpoint 81k

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.

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