Cleanadaptors Vs Cutadapt Vs Trim_galore

Question

[Shicheng Guo]

Hi All,

Any comments to Cleanadaptors Vs Cutadapt? Which one is better? Any big difference?

It seems Cleanadaptors can accept whole illumina adaptors and primers as the input (200 adaptors and primers).

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Thanks.

[pld]

Test them and see what works best for you!

Answer 1

[GenoMax]

I like BBDuk from BBMap. Brian Bushnell, developer of BBMap, supplies all common adapters in a single file in the "resources" directory.

[Brian Bushnell]

So do I :) Also, my tests indicate that it's faster:

Answer 2

[biofalconch]

Also maybe you want to check out Trimmomatic, as far as I know you can feed it a list of adapters to cut as input, as well as other functions.

http://www.usadellab.org/cms/?page=trimmomatic