pipeline optimization for NextSeq vs Hi/Miseq

[klebsiella]

Dear all,

I heard comments lately, from two sources, that NextSeq 500 "requires extensive bioinformatics pipeline optimization and it has been very challenging for most labs with experience in NGS Illumina technology".

I personally believe they mean the bcl2fastq conversion, since both platforms use different chemistry. However, I want to know from you if any downstream analysis, following the generation of the fastq file, needs a special bioinformatics treatment or is challenging, as both sources claimed.

For me, I am not sure why treating a fastq file will differ either it is generated by NextSeq 500 or HiSeq or MiSeq !!!

Any comments/clarifications are much appreciated,
All best and thanks,

[Brian Bushnell]

Downstream analysis of NextSeq data is no different from HiSeq or MiSeq data; I have no idea what they're talking about. Of course, it's much lower quality, but sometimes HiSeq data comes out low-quality, so a robust pipeline for processing HiSeq data will process NextSeq data with no issues. There will be additional false-positive variant calls, inferior assemblies, additional noise in analyses, and all the other expected effects of using low-quality data, but that just means your results will be worse, not that the pipeline needs to be any different. Oh, and of course the header format is completely different again, but any pipeline that depends on a specific Illumina header format is just asking for trouble.