Consensus

Librairies

• https://github.com/ksahlin/NGSpeciesID
• https://github.com/asrivathsan/ONTbarcoder

How to run the sequence_preprocessing.py script

The Anaconda environment used to run the sequence_preprocessing script can be found in the file GenoRobotics_bioinfo_consensus.yml
Here are the following steps to follow to run it:

• open the current folder in your terminal
• type conda env create -f GenoRobotics_bioinfo_consensus.yml in the terminal to create the environment GenoRobotics_bioinfo_consensus (Anaconda must be installed)
• type conda activate GenoRobotics_bioinfo_consensus in the terminal to activate the environment
• type cd src in the terminal
• type python sequence_preprocessing.py in the terminal to try to run the main loop of sequence_preprocessing.py

If everything can be run, it means that the environment is correctly installed.
Well done, you have successfully preprocessed your first dataset ! Now you can try to play with other datasets with different parameters. 👍

Notes

Currently, a small dataset called rbcL_Qiagen_tomato_5000.fastq (containing 5000 sequences, ~5 MB) can be found in the src folder. This is a sampled version from the entire dataset rbcL_Qiagen_tomato.fastq (containing ~200k sequences, ~204 MB). This dataset is used in the main loop of the sequence_preprocessing.py script in the run example and can be used to check if the environment is correctly installed.

The current version of the sequence_preprocessing.py is a test/incomplete version and everything is subject to change.