Using two sets of Illumina reads to assembly geome using AutDeNovo pipeline

[augustinaloewenstein]

Hey Martin,

I would like to assemble a genome using the AutDeNovo pipeline while combining two sets of Illumina data (= set 1 fwd&rev + set 2 fwd&rev = 4 read files).
Should I pair each set so to have 2 read files or can I tell the pipeline that there are 4 files now?

Thank you,
best wishes
Augustina