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Old 09-12-2018, 03:09 AM   #1
JMir
Junior Member
 
Location: barcelona

Join Date: Sep 2018
Posts: 1
Default Create CSS with different adapters

Hi!

I've searched for a similar thread and wasn't able to find a solution so I hope that this question is not repeated.

I am sequencing some SMRT library that contains the PacBio SMRT sequencing adapter in one end of the reads and a different adapter in the other.
I would like to create a CCS from these and I haven't been able to find any software that helps me doing that.

I have been looking to SMRT Link, which works only with SMRT adapters. Is there a way to introduce a custom adapter sequence?
I have also tried BBMap but I could only trim the adapters that are on the ends of the reads, not on the middle of them in order to create the CCS.
I was thinking on generating a custom script to do that but I find some difficulties like the mutation of sequencing, etc.

Can someone help me to find a useful software for my problem?

Thank you very much!!
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adapter remove, ccs, smrt

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