short read data

[rmormando]

I have Illumina short-read sequences I want to use as an input will the tool take that into account when creating a database?

The samples are labeled asSample1_R1.fasta Sample1_R2.fasta would I put that all into the input list file so it reads like:

Sample1_R1
Sample1_R2
Sample2_R1
Sample2_R2
....
Sample20_R1
Sample20_R2

Would the tool recognize short read inputs? Or should I merge the two files so it only takes one input for that particular sample?