test dataset for MinIon algorithm development

Question

[ccagg]

Hi,

Can anyone point me to a test dataset that contains raw picoAmp data generated by the Oxford Nanopore MinIon platform? I am interested in algorithm development for this type of data but I would like to get a sense of the data before we begin sequencing on our own MinIon. My problem currently is that I am finding mostly very large, whole genome sequencing data. I would ideally like just a gene or a small region for testing purposes.

Thanks!

[WouterDeCoster]

raw picoAmp data

So, fast5 format?

[ccagg]

Yes. Not looking for fastqs that are already base-called

[WouterDeCoster]

Is an ecoli genome too big?

[ccagg]

Yeah I guess the fast5 files are ~500GB, I was hoping for something on <5GB just to test some ideas out

[cookie123]

Thanks, but the data is missing here http://s3.climb.ac.uk/nanopolish_tutorial/ecoli_2kb_region.tar.gz

I am looking for a small dataset like this one to test my code. Can anyone help please?

[GenoMax]

This tutorial has a few example datasets: https://denbi-nanopore-training-course.readthedocs.io/en/latest/data.html

Answer 1

[WouterDeCoster]

This nanopolish tutorial has a small set of fast5 files from ecoli.

You can get it using

wget http://s3.climb.ac.uk/nanopolish_tutorial/ecoli_2kb_region.tar.gz