Jupyter Notebook used for bar-seq library analysis in Bleuven et al 2019. See the manuscript and the notebook for specific program requirements.
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The raw sequencing files should first be downloaded and put in same directory as the notebook, and then renamed to "A.Dube_Cabsoil_p01_c01.fastq.gz".
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Calls to trimmomatic and fastqc should are included in the notebook but should be run in the command line if subprocess.check_output() is not used in the notebook cell
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The script processes reads in two batches to avoid completing busting up the RAM capacity of the computer. The notebook ran on a Ubuntu machine with 32gb RAM, use lower memory at your own risk