Illumina Reads - Influenza H3N2 - Which parameters?

[LauraVP1994]

Dear,

I am very interest in using your tool for my project. I'm working on influenza reads that were sequenced with Illumina MiSeq. I was able to extract quasispecies with LoFreq, however LoFreq doesn't have the ability to construct haplotypes, therefore I turned to this tool.

I was wondering if there is somewhere some more information about the parameters? Or could you give some indication what would be “good/appropriate” parameters. Also influenza is a segmented genome, is it possible to run this tool for the whole genome (so fasta file has 8 fasta sequences) or should this then be done per segment?

Kind regards and thanks in advance!
Laura