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Cleanadaptors Vs Cutadapt Vs Trim_galore

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.

trim_galore cutadapt adaptor
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updated by Ram Ram • written by Shicheng Guo Shicheng Guo

Test them and see what works best for you!

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written by pld pld

2 answers

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

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written by GenoMax GenoMax

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

Speed

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updated by Ram Ram • written by Brian Bushnell Brian Bushnell

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

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written by biofalconch biofalconch

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