Sanchez-et-al.-2017-Nature-Communications

Workflows

These were the workflows for solving several bioinformatic analysis for Sanchez et al. (2017) Nat Comm.

I used standard open-source software in Linux command-line, and custom-made python scripts (I kept here the original names of the python script's files to match my records)

It also involved some manual organization of files, manual assessment of results and manual processing to reach final result (e.g.sequence reconstruction).

Although it solved the problems faced at the time, note that this is a beginner's code, as I'm not a professional bioinformatician or data scientist.

As such, it may probably look overly complicated; and other more advanced solutions are likely simpler or more effective.

The workflow also display some historical contingencies, as I was learning while doing.

None of this work would be possible without the collaboration with Herve Gaubert, and the kind bioinformatics support of Varodom Charoensawan, Hugo Tavares, Jeremy Gruel, Hajk-Georg Drost, Anna Gogleva and Yassin Refahi.

Diego H. Sanchez (diego.sanchez@slcu.cam.ac.uk)