MinION fast5 to fastq

Finally, I got my first data from MinION. The first obstacle I found is the native MinION format, Fast5. Most programs require FastQ. Luckily there are poretools, which makes conversion Fast5 –> FastQ very easy.

# install poretools
sudo pip install poretools

# convert fast5 to fastq
poretools fastq fast5/ > out.fastq

If you want to achieve better basecalling accuracy, have a look at DeepNano: alternative basecaller for MinION reads. It achieves better basecalling accuracy than native MinION basecaller for both 1D (~7%) and 2D (~2%) reads.

4 thoughts on “MinION fast5 to fastq

  1. Hello,

    We recently finished a MinION sequencing experiment and got our first fast5 files. We are having difficulty converting them to fastq files. Would you be able to send some pointers on how we can do the conversion? I would greatly appreciate your help.

    Thanks and best regards,

  2. It does not work to me. After the command poretools fastq fast5_files/ > out.fastq, this file is empty. Please, could you help me?

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