Don’t let your unmapped reads go to waste
The ROP protocol is available for free download as a package that is easy to install and run. It provides a one-command solution to discover the source of all unmapped reads, which originated from complex RNA molecules, recombinant B and T cell receptors and microbial communities.
ROP provides a flexible interface that allows users to perform analysis of interest, rather than running a full ROP analysis. For example,
--microbiome option allows running only microbial analysis.
See the main webpage https://github.com/smangul1/rop/wiki