Monitor tool for nanopore sequencing runs. It is used to estimate the long read coverage on a short reads assembly while sequencing
THIS IS THE ALPHA VERSION. It is published as it was used for the first test. A beta version will soon be released
- Python3.6
- Deepnano-blitz (it is run in a conda environment with Python 3.6 and the Rust compiler)
- blast+
- biopython
- numpy
conda activate deepnanoblitz
python NanoPoor.py {folder_name} {reference_assembly}
the {folder_name} is the same as the one set in the MinKNOW software
{reference_assembly} needs to be in fasta format
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NanoPoor uses deepnano-blitz to perform a quick-and-dirty basecall
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the output fasta file is used as query in a blast-search against the short-read assembly
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this process is run every few minutes (default: every hour) on newly generated fast5 files and updates a dictionary containing the covarege for each base in the draft assembly
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NanoPoor performance is optimal when run using 10+ threads in a RAMdisk folder
- needs a better implementation of the deepnano-blitz basecaller
- needs parameter settings and a help menu
- needs a graphical output
- needs to automatically detect an ongoing nanopore run