Soap denovo input files in contig file from FLASH

[mafireyi]

I am using Soap denovo for whole genome assembly. I have use trimmonatic and Flash to trim and merge my reads. Flash spits out 4 output files. My question is which of the output files from Flash should I use in the config file of Soap. Should i include the out.notCombined files together with out.extendedFrags file.

Thanks

[GenoMax]

Solution on Biostars: https://www.biostars.org/p/150182/

[Brian Bushnell]

In my experience, merging reads leads to an inferior Soap assembly, at least for metagenomes. I'm not sure why. I suggest you try both ways (merged and unmerged).