Questions tagged [fast5]

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single_to_multi_fast5 does not collect all the single files if the input folder contains mixed types of fast5 files

I have a dataset that contains thousands of mixed multiple and single fast5 files in a non-homogenous folder structure. The reads and fast5 files are coming from different labs and some labs gave ...
Marjan's user avatar
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1 vote
1 answer
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Reading a Fast5-file with Python

I am trying to extract data from fast5-file with python 3.9.13 in Ubuntu. I have found a library "fast5_research"(This package comprises an API to HDF containers used by the research groups ...
Shwarz's user avatar
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3 votes
2 answers
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Understanding fast5 format

I would like to reproduce the results on figure 1 from THIS publication. I downloaded the data and explore it with h5ls and h5dump based on HDF5. I would like to understand: ...
aerijman's user avatar
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1 vote
1 answer
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Oxford nanopore promethion; does guppy3 separate fast5 into pass and fail? If not what does?

just a quick question about fast5 pass fail folders. I have been working under the assumption that the fast5 pass fail folders I was given as raw data from our ONT vendor came from them doing base ...
Liam McIntyre's user avatar
1 vote
1 answer
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How do you map nanopore fast5 files?

Is there a best practices for mapping Oxford Nanopore files to a reference? Is there a tool that can take a tarball of fast5 files and map them directly or do they need to be converted to fastq first?...
juniper-'s user avatar
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5 votes
2 answers
2k views

How to get Nanopore MinION fast5 from SRA

I found some Nanopore MinION data on SRA, which I would like to investigate. I use sratoolkit for Illumina data all the time, but I am not sure how to get the ...
benn's user avatar
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13 votes
2 answers
3k views

How to convert fastq to fast5

fast5 is a variant of HDF5 the native format in which raw data from Oxford Nanopore MinION are provided. You can easily extract ...
aechchiki's user avatar
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