small dataset for NGS pipeline

Question

[JoeDoasi]

Dear bioinformaticians,

I would like to know if there is a small NGS raw data that can be used for analysis on a private PC.

The aim is to evaluate my pipeline (alignment, variant calling, annotation) and see if all commands are working before moving to the HPC.

Appreciated, Yousef

[finswimmer]

Hello,

have a look at the European Nucleotide Archive for finding data that fits your needs. Maybe a sample of this study?

fin swimmer

[Bastien Hervé]

Along to @finswimmer's comment, to download from ENA Fast download of FASTQ files and metadata from the European Nucleotide Archive (ENA)

[JoeDoasi]

Hello,

Thank you for your reply.

This is a good start. I will try it.

[WouterDeCoster]

a small NGS raw data

You may want to elaborate on:

• organism of interest (human?)
• sequencing technology (illumina?)
• size of dataset

[JoeDoasi]

I actually would like to know if there is clinical exome data available!

do you think clinical exome data will be exhaustive for the private PC?

thanks

[Bastien Hervé]

Why not take data attached to the publication of your interest ?