bowtie2 and FLASh

Question

[Fedster]

I was wondering whether there is a proper way of using bowtie2 after going through my reads with FLASh (https://ccb.jhu.edu/software/FLASH/). Flash would produce 3 files:

• extended fragments
• non extended R1 fragments
• non extended R2 fragments

I could call bowtie2 twice (one for the extended fragments, one for the R1/R2 reads) and then merge the two sam (or bam) files, though I get the feeling the -U option in bowtie2 might allow me to do something smarter? am I missing something? being able to input all 3 files at once would be faster/simpler, and thus preferable if possible (I accept it might not).

[gb]

I would say: or you use only extended fragments or you do not use FLASH.

But besides this, maybe this helps Should I merge forward and reverse reads before mapping

[Fedster]

I asked Julian Catchen (who wrote Stacks) and he recommends NOT using it.