Question: test dataset for MinIon algorithm development
0
gravatar for christacaggiano
2.5 years ago by
UCSF
christacaggiano50 wrote:

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!

sequencing nanopore • 1.0k views
ADD COMMENTlink modified 2.5 years ago by WouterDeCoster44k • written 2.5 years ago by christacaggiano50

raw picoAmp data

So, fast5 format?

ADD REPLYlink written 2.5 years ago by WouterDeCoster44k

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

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by christacaggiano50

Is an ecoli genome too big?

ADD REPLYlink written 2.5 years ago by WouterDeCoster44k

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

ADD REPLYlink written 2.5 years ago by christacaggiano50
1
gravatar for WouterDeCoster
2.5 years ago by
Belgium
WouterDeCoster44k wrote:

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
ADD COMMENTlink written 2.5 years ago by WouterDeCoster44k
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