Associated code for: Next-generation data filtering in the genomics era
This repository contains the supplementary workflow notebooks for the paper Next-generation data filtering in the genomics era, DOI: 10.1038/s41576-024-00738-6, and the associated scripts necissary to run them on a unix-based file system.
It also contains the the scripts used to produce the figure in Box 2 and the figures in the Supplementary material.
To view the workflow notebooks, go to main/workflow_notebooks/ and select either:
Pre-knit versions of these are also available for the pre-variant and post-variant workflow notebookss as well from these links or in the same directory as the .rmd files. These can be downloaded and viewed with most web browsers.
Each of the shell (.sh) scripts in main/workflow_notebooks/ are also necissary for pre-variant notebook, and should be downloaded and placed in the working directory. All other dependencies are described in the notebooks.
Lastly, the scripts needed to produce the Box 2 figure are all contained at /main/scripts, with the steps required to prepare the raw data and produce the figures described in Box_1_figure_and_SI.Rmd. Some of the shell (.sh) scripts are written for our slurm for our specific computing cluster and may need to be tweaked for other systems.