Questions: Parameters & Functionality

[a-kroh]

Hi Martin,

• Can the pipeline be run with uncompessed files as well or will it result in an error?
• Can individual steps be skipped with some parameter flags (e.g. no QC or no trimming if these steps have already been performed)
• Does trimming take the QC results in account (the intro text seems to suggest this, but it is not clearly stated)
• Does the pipeline also work with interleaved files as downloaded from NCBI SRA (if yes, what is the syntax needed)
• Which steps are paralellized and which are not (maybe add a flowchart illustrating this)
• Can expert parameters be defined for individual steps in the pipeline (e.g. trimming, assembly)?

Kind regards Andreas