Question: Merging Paired-end Reads for Metagenomics
gravatar for gtasource
29 days ago by
gtasource20 wrote:

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?

sequencing • 144 views
ADD COMMENTlink modified 5 days ago by Biostar ♦♦ 20 • written 29 days ago by gtasource20

You should merge the data before you do other manipulations. There are multiple software packages that can do the merging. from BBMap suite is one. A guide is available here.

Other tools in this category are FLASH, PEAR, COPE, Prinseq.

ADD REPLYlink modified 29 days ago • written 29 days ago by genomax73k

I really appreciate your response! I will look into BBMap and the bbmerge option. Cheers!

ADD REPLYlink written 29 days ago by gtasource20
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