Microbiome Science Informatics Resources - Updated Autumn 2024

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1	Topic	Description	Category	Link
2	UNIX/linux	A guide for learning how to navigate the terminal on computers. Teaches all basic commands and assumes no prior knowledge.	Linux	https://swcarpentry.github.io/shell-novice/02-filedir.html
3	OSC linux tutorials	Tutorials through OSC on how to use linux basics	Linux	https://www.osc.edu/documentation/tutorials/unix_basics
4	Cornell Virtual Workshop	A one-stop-shop web-based training platform developed by Cornell Advanced Computing group. Here you can learn linux basics, intros to python, R, best practices for programming, debugging, code optimization, SLURM, how to use GPUs, data science basics, and how to optimally run jobs on the supercomputer	Linux, R, Python, Batch System	https://cvw.cac.cornell.edu/Roadmaps/
5	OSC new user training	A video guide (with transcript) for anyone new to OSC. Provides an overview of the supercomputing resources available and services OSC provides	Batch System	https://www.osc.edu/content/new_user_training
6	Batch limits	For anyone wanting to run a job (submit a program to be run on the supercomputer), reviewing the batch limits here will allow you to configure your SLURM script for optimal running depending on which supercomputer (owens or pitzer) you choose.	Batch System	https://www.osc.edu/resources/technical_support/supercomputers/owens/batch_limit_rules https://www.osc.edu/resources/technical_support/supercomputers/pitzer/batch_limit_rules
7	How to use the batch system	A free self-paced course to learn about how to use OSC's batch system.	Batch System	https://osc.catalog.instructure.com/courses/batch-system-at-osc
8	linux time-saving shortcuts	A selection of shortcuts in unix curated by OSC that will speed up your linux coding!	Linux	https://www.osc.edu/documentation/tutorials/unix-basics/unix-shortcuts
9	Tar tutorial	arr	Linux	https://www.osc.edu/documentation/tutorials/unix-basics/tar-tutorial
10	SLURM batch job tutorial	A tutorial for how to write a SLURM batch job. Goes through basic SLURM jobs, teaches you how to run parallel jobs, and also how to write job arrays for doing multiple of the same program on different inputs efficiently.	Batch System	https://docs.rc.uab.edu/cheaha/slurm/slurm_tutorial/
11	R	Tutorials for learning R from scratch. The youtube tutorials are an all-in-one multi-hour videos. The R-for-beginners textbook is also here and is a great code-along guide.	R	https://www.youtube.com/watch?v=_V8eKsto3Ug https://cran.r-project.org/doc/contrib/Paradis-rdebuts_en.pdf https://www.youtube.com/c/RiffomonasProject/featured
12	Visualization in R	A decision tree for figuring out which type of visualization to use based on the type of data you have A collection of community submitted R graphs to help find different ways to visualize your data. Complete with code. A great resource for thinking about different visualization possibilities	R, data visualization	https://www.data-to-viz.com/ https://r-graph-gallery.com/
13	Jupyter Notebooks	How to use jupyter notebooks. Jupyter notebooks are a way of coding in python that allows for enhanced readability and iteration of code. They also make it very easy to share your code when finished with a project in a way that is readable for others.	Python	https://www.youtube.com/watch?v=HW29067qVWk
14	RMarkdown	How to use Rmarkdown, a program that allows R to be run in "chunks" and prints the output of each chunk below. These are advantageous over scripts when wanting to document and share your code with others more easily.	R	https://www.youtube.com/watch?v=DNS7i2m4sB0
15	Viral identification with VirSorter2	For identifying viruses from assemblies, please refer to this guide on the correct way to use VirSorter2	virome	https://www.protocols.io/view/viral-sequence-identification-sop-with-virsorter2-5qpvoyqebg4o/v3
16	Viral identification with genomad	For identifying viruses from assemblies, please read through this guide, especially the post-classification filtering to understand how to use genomad. Genomad is faster and more easy to use than VirSorter2, and identify similar viruses.	virome	https://portal.nersc.gov/genomad/pipeline.html
17	Microbiome data analysis and visualization playlist	A collection of youtube tutorials from Pat Schloss (Umich) on how to do microbiome data analysis and visualization in R. Requires looking through the playlist to find the right video for your task.	microbiome	https://www.youtube.com/watch?v=D6CunpqF04E&list=PLmNrK_nkqBpIIRdQTS2aOs5OD7vVMKWAi
18	Organizing informatics projects	A short article on how to organize your bioinformatics projects. Highly recommended to develop some way to organise your files, a consistent naming system (under_scores, camelCase, dash-es). Will make it much easier to share your work with others and not waste time looking for files!		https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424
19	Pandas Tutorial	A tutorial for using Pandas, the data science package for python	Python	https://www.youtube.com/watch?v=5JnMutdy6Fw
20	Getting started with conda environments	How to use conda environments, which allows you to use programs that require different versions of various programs (called dependencies). For example, if I want to use a program that requires R 3.4, and then another program that requires R 4.0, I would have to create separate conda environments for each of these programs so that they can be run without having to change my version of R in-between. One program may seem trivial, but sometimes you have two programs with hundreds of different dependencies, and this is where environments come in handy, or else you will have to keep changing which versions you have in your local and eventually won't be able to run programs correctly.	Environments	https://www.youtube.com/watch?v=YJC6ldI3hWk
21	Managing multiple conda environments	Tutorial for managing multiple conda environments and switching between them, updating them, etc.	Environments	https://www.youtube.com/watch?v=cY2NXB_Tqq0
22	Anaconda Navigator	Anaconda Navigator is a graphical user interface and hub for many programs useful in python programming. Examples are Jupyter Notebooks, Spider (RStudio-like GUI for python), and anaconda environment manager	Environments	https://docs.anaconda.com/navigator/
23	MAVERIC Lab Informatics Wiki	A wiki primarily used by members of the Sullivan and Rich labs with template scripts and usage instructions for running hundreds of different software programs for microbiome analysis. Contains useful information about different programs with a nice search function, all formatted for running on the Ohio Super Computer		https://maveric-informatics.readthedocs.io/en/latest/
24	Statistical Analysis for Microbial Ecology	GustaMe is a one-stop-shop for microbial ecology statistics	Statistics, microbiome	https://sites.google.com/site/mb3gustame
25	Bioinformatics Virtual Coordination Network	training to helping wet-lab biologists pick up some computational skills/begin computational projects	Linux, R, metagenomics, Python, transcriptomics, functional annotation, amplicons	https://biovcnet.github.io/
26	Microbiome Informatics Webinar Series	Genome-resolved microbiome informatic 2+ hour hands-on webinars	microbiome	https://coms.osu.edu/webinars/microbiome-informatics-webinar-series
27	Microbiome Center Consortium Education Resource	a collection of training links specific for microbiome scientists	microbiome	https://microbiomecenters.org/education-resources/
28	R for Data Science	book	R	R for Data Science
29	Python for Data Science	book	Python	Python Data Science Handbook
30	Phyloseq	Learn to use Phyloseq, an R package that combines OTU abundance tables with taxonomy and metadata for ecological statistics	microbiome, R	Phyloseq tutorial
31	ANCOM-BC2	Tutorial for employing ANCOM-BC2. Useful to do the phyloseq tutorial first. A state-of-the-art and robust program for determine which OTUs are differentially abundant	microbiome, R	ANCOM-BC2 Tutorial
32	OSC Community Tools: installed as singularity images
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