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.


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