(Nucleomics-VIB)

This Snakemake pipeline and accompanying RStudio report are largely inspired by the ont_tutorial_pinfish found at nanoporetech with addition of a few analysis steps.

Please refer to the original document for installilng the necessary components and for more info about the pipeline.

Running this code requires:

• installing miniconda and all required dependencies from the provided environment.yaml (conda env create --name pinfish_3.6 --file=environment.yaml)

• editing the config.yaml file to match your own machine, reference genome, and data

• adding the required data files in due locations (matching the yaml)

• edit the Preamble.md file to include a text describing the 'Aim' of the experiment. This text will be added to the report as first section and is one of the two report sections that can be edited by the end-user.

• edit Conclusion.md that will be added at the end of the report during knitting.

• run Snakemake with snakemake --use-conda -j <thread number>

If all goes well, the proper analysis will be followed by the making of the html report using Rmarkdown and conversion to a html report file with pictures and tables.

• the final data files are put in the folder Analysis
• the final report should appear as Nanopore_Pinfish_Analysis.html. This report is a single html file with all in it and can be sent to customers/colleagues as a final report. It is nicer than a PDF version because of large tables and figures which would suffer from page breaks and it can be viewed on any device supporting html (incl smartphones :-).

view the report hosted here

rem: when something breaks the snake, or if you add more text/comments in the initial Rmd report, you can regenerate the report manually with R --slave -e 'rmarkdown::render("Nanopore_Pinfish_Analysis.Rmd", "html_document")' within the base project folder.

This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.