Question: PhiX forward and reverse reads for MiSeq and NextSeq Platform
gravatar for kspata
6 months ago by
kspata50 wrote:


I am in process of validating a pipeline for data pre-processing, align to reference and variant calling. I am interested in using the PhiX data from Basespace. But I can not find the raw sequence forward and reverse reads anywhere on Basespace. How can I obtain the Paired end data for both MiSeq and NextSeq platform to use as input files for the pipeline?

The purpose of the pipeline is to work on bacterial and viral genomes to find variants.

Are there any other gold standard databases to use to validate the pipeline?


sequencing next-gen illumina • 293 views
ADD COMMENTlink written 6 months ago by kspata50
gravatar for genomax
6 months ago by
United States
genomax69k wrote:

Looks like Illumina does not share the original fastq data for phiX datasets in BaseSpace.

How about these datasets from ENA MiSeq, NextSeq 500 and HiSeq 2000? If you have a local sequencing facility they may have data from phiX validation runs you could get access to.

ADD COMMENTlink modified 6 months ago • written 6 months ago by genomax69k

Thank You genomax!! I did contact Illumina, and was informed that the data is not available for NextSeq and MiSeq. I plan to use the data from the above links for validation. Which reference sequence should I use for mapping? I have found the following link:

Will this be a correct link to use?

ADD REPLYlink written 6 months ago by kspata50

Illumina provides sequence in their phiX bundle on iGenomes site here.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax69k
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