Best tool for quality trimming at 5 prime?

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5.2 years ago

crespialba ▴ 20

Which is the best tool to perform a quality trimming at 5 prime end? I have a sample with some sequences with low quality at the the beginning (as well as at the end) and I want to trim those parts with low quality.

sequencing quality-control next-gen • 1.1k views

ADD COMMENT • link updated 5.1 years ago by Biostar 20 • written 5.2 years ago by crespialba ▴ 20

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I believe nearly all quality-trim tools can do this (trimmomatic, BBduk, ... to name a few)

Question is if you should be doing so .....

ADD REPLY • link 5.2 years ago by lieven.sterck 15k

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As @lieven said all tools should do the basic quality based trimming. Some may allow you to do a windowed approach (saving some additional bases). Not sure if all tools will but bbduk can.

ADD REPLY • link 5.2 years ago by GenoMax 142k

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Cross-posted on SE

ADD REPLY • link 5.2 years ago by ATpoint 82k

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