How to remove all recombinant viral sequences from given multi fasta file

Question

[rajeshkumar_vinod]

Hello,

I tried RDP (Recombination Detection Program) to remove recombinant sequences from a multifasta file. after excluding recombinant sequences when i re-ran RDP on sequences kept after first run, I again get some recombinant sequences.

Is there any way to remove all recombinant sequences in one run or I will have to re-run RDP until it doens't detect recombinant sequences anymore?

Thank You.

[Kevin Blighe]

Have you tried something very simple such as cutadapt (http://cutadapt.readthedocs.io/en/stable/guide.html)?

In its most basic syntax, you can trim any recognisable sequence from your sequence files:

cutadapt -a AACCGGTT -o output.fastq input.fastq

In the options, I think that you can specify the program to remove any reads that contain the identified sequence.

If you have a known list of recombinant sequences, I think that cutadapt also allows you to specify a file with a list of sequences to remove.

Kevin