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Does anyone know of a tool to convert fast5 data to fastq?
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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:
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, 08:45 AM. -
Sorry, the mentioned script generates FASTAs. But upon replacing "fasta" with "fastq" in line 17 it will generate indeed FASTQ files.
Originally posted by luc View PostComment
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There's a five line python script in the Metrichor docs that shows you how to do this.Comment
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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?.Originally posted by Bukowski View Post
Nick's script has some advantages there.Comment
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I had problems installing the hdf5 python libraries, so resorted to PDL::IO::HDF5 and Perl.Originally posted by luc View PostComment
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