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Old 06-19-2014, 02:38 PM   #1
Brian Bushnell
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Default fast5 to fastq converter

Does anyone know of a tool to convert fast5 data to fastq?
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Old 06-19-2014, 04:36 PM   #2
luc
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I do not understand the the fast5/hdf format very well. Most likely such a converter is not universal? Here is one:

https://gist.github.com/nickloman/3345d05e3a4642b5306c

This certainly needs to be amended if the data are located in other "directories" of the fast5 file when using a different pipeline.

Last edited by luc; 06-20-2014 at 08:45 AM.
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Old 06-19-2014, 09:52 PM   #3
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Sorry, the mentioned script generates FASTAs. But upon replacing "fasta" with "fastq" in line 17 it will generate indeed FASTQ files.

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Originally Posted by luc View Post
I do not understand the the fast5/hdf format very well. Most likely such a converter is not universal? Here is one:

https://gist.github.com/nickloman/3345d05e3a4642b5306c
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Old 06-20-2014, 08:28 AM   #4
Bukowski
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There's a five line python script in the Metrichor docs that shows you how to do this.
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Old 06-20-2014, 08:41 AM   #5
luc
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Quote:
Originally Posted by Bukowski View Post
There's a five line python script in the Metrichor docs that shows you how to do this.
Yes, but these 5 lines are not a complete script and they do not seem to work very well - this might be a problem on my side?.
Nick's script has some advantages there.
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Old 06-20-2014, 08:49 AM   #6
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Quote:
Originally Posted by luc View Post
Yes, but these 5 lines are not a complete script and they do not seem to work very well - this might be a problem on my side?.
Nick's script has some advantages there.
I had problems installing the hdf5 python libraries, so resorted to PDL::IO::HDF5 and Perl.
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