fast5 to fastq converter

[Brian Bushnell]

Does anyone know of a tool to convert fast5 data to fastq?

[luc]

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.

[luc]

Sorry, the mentioned script generates FASTAs. But upon replacing "fasta" with "fastq" in line 17 it will generate indeed FASTQ files.

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

[Bukowski]

There's a five line python script in the Metrichor docs that shows you how to do this.

[luc]

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.

[Bukowski]

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.