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Groomer function strictly necessary for all NGS jobs?

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.

rna-seq
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updated by GenoMax GenoMax • written by blewettn • blewettn

1 answer

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).

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written by GenoMax GenoMax

Thanks very much for your detailed response!

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written by blewettn • blewettn

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