Merging Paired-end Reads for Metagenomics
I have some metagenomic shotgun sequencing data that is paired-end. I am considering using metaphlan2 and the biobakery workflows for analysis. However, the documentation states that they recommend merging the paired-end sequencing data into one before beginning the analysis. My question is:
1.) Should I merge the sequencing data and the trim them? 2.) Should I trim and then merge? 3.) How do I merge the datasets?
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You should merge the data before you do other manipulations. There are multiple software packages that can do the merging.
bbmerge.shfrom BBMap suite is one. A guide is available here.Other tools in this category are FLASH, PEAR, COPE, Prinseq.
I really appreciate your response! I will look into BBMap and the bbmerge option. Cheers!