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Access to bulk FAST5 datasets

I am looking to try out some different methods for ONT adaptive sampling, starting by running some playback experiments. Anyone know where I can download some bulk fast5 files? Specifically interested in viral sequences.

ont sampling nanopore adaptive
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written by matt_arnold_bio • matt_arnold_bio

1 answer

Here is one SRA project that uses "adaptive sampling": https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1314197 Looking at the data for a couple of samples, they do not seem to provide fast5 files.

Here are some random examples of fast5 datasets (they are not for adaptive sampling) :

ONT makes some test datasets available (at least one contains fast5 files): https://registry.opendata.aws/ont-open-data/

Some test data here: https://figshare.com/articles/dataset/Example_dataset_containing_Fast5_and_BAM_files/26093869?file=48273898

You will also find fast5 files in Data Access tab of some SRA datasets (depending on if the submitters have posted them). Here is one example: https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR8767349&display=data-access

fast5 is a legacy file format. POD5 is the current format in use: https://nanoporetech.com/document/data-analysis#file-formats

Were you not able to make the test data on readfish site work?

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written by GenoMax GenoMax

Hi there! Thanks for the reply! Yes, I could use the data on the readfish tutorial. I was just wondering where I might look for something that was a bit more applicable to my specific use case, but there is a dataset on the nanopore/epi2me site that you link that I think should be suitable.

I guess I'll find out when I try it but does POD5 automatically support simulated playback in MinKNOW?

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written by matt_arnold_bio • matt_arnold_bio

does POD5 automatically support simulated playback in MinKNOW?

I have no idea. You can try it out though.

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written by GenoMax GenoMax

Just bumping this to see if anyone knows where I can download example bulk files (i.e. files containing metadata allowing simulated playback in MinKNOW) ideally from experiments targeting viruses?

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written by matt_arnold_bio • matt_arnold_bio

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