Assembly of partial rRNA sequences

[justinmaire]

Hello!

I am wondering if there is an option to recover only partially assembled rRNAs sequences?
This is the command line I'm using at the moment:
phyloFlash.pl -lib 16S_${i} -read1 R_1 -read2 R_2 -almosteverything -readlength 100

In the output I am only getting full-length rRNA genes. Lots of possible rRNAs should be in my reads (and get mapped by phyloFlash), so I was hoping I could recover those even if only partial?

Thanks!
Justin