Groomer function strictly necessary for all NGS jobs?

Question

[blewettn]

I am wondering if the Groomer tool is a strictly necessary step after BCL to FASTQ conversion with an Illumina Nextseq500 output, or if it is used for converting sequencing files from less-utilized platforms? I'm building my workflow and don't want to use unnecessary resources.

Answer 1

[GenoMax]

If you are asking in the context of galaxy then perhaps it may only be essential to identify a dataset as sanger fastq format (phred+33) (though I thought one could edit that information directly using the pencil icon and choosing the dataset format as fastqsanger, sorry I have not used galaxy recently).

Edit: This page indicates other functions that fastq groomer may be doing in Galaxy.

Data generated by illumina sequencers for the past 3+ years has been in sanger fastq format and as such does not require "grooming" (outside of galaxy).

[blewettn]

Thanks very much for your detailed response!