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Analysis of paired-end GBS data

Hi there!

I'm working on GBS data analysis of plants with available reference genome. I already tried Tassel 5 GBS v2 pipeline (https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline) and it performed quite well on our data. The main issue that Tassel doesn't accept paired-end (PE) data that we alredy have got. Would you advise me an efficient pipeline for GBS data analysis that's able to handle Illumina PE data please?

next-gen snp genome
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written by Denis Denis

Have you got any solution to above mentioned problem?

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written by Tm Tm

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