Welcome to MAVERIC Informatics documentation!

Welcome to the Microbial and Viral Ecological Research in Columbus Informatics website!

This site serves as a common portal to a variety of resources primarily handled by members of the Sullivan lab.

At this site you’ll find information relating to:

• The OSU Environmental Microbiology “eMicro” efforts on OSC

• The OSU Microbiome Informatics course (M8161) (more below)

• A public-facing portion of the Sullivan lab’s informatics wiki, primarily focused on viral ecology research

Please keep in mind that this guide is very much a work in progress!. It is being built, week-by-week, as the microbiome informatics course is taught during the Fall of 2023. Every week (and often, daily) this site will be updated, built upon the lectures of M8161, with the goal of providing sufficient information to support class projects and research overall.

Contents:

• Introduction and Overview
• Microbiome Informatics (M8161)
• UNIX/LINUX Introduction and Guide
  • Basic Navigation and Universally Common Commands
  • The Profile (aliases, environmental variables, $PATH)
  • File and Folder Permissions
  • Advanced (or maybe “convenient”?) commands
• OSC Introduction and Guide
  • Systems
  • Login Nodes
  • Filesystems
  • Connecting to OSC
  • Transferring Data to/from OSC
  • Batch Processing (i.e. submitting jobs)
  • Modules
  • Links
  • Job Arrays
• QIIME2
  • Data Import
  • Demultiplexing
  • Summarize
  • Quality Control and Creating the Feature Table
  • Alpha and Beta Diversity Analyses
• Building Modules and Tools on OSC
  • Directly
  • Modules
  • Singularity
• Available Environmental Microbiology (“eMicro”) Apps and Tools
  • Quality Control [of Reads] and Read Mapping
  • Assembly
  • Binning
  • Gene Callers
  • Annotation and Analyses
  • Virus Analyses
  • Phylogenetics
  • Miscellaneous
• Modules and Tools on OSC
  • Running Tools
• R
• End-to-End Processing of a Microbial Metagenome
  • Downloading the data
  • Read Quality Control
  • Read Quality Control (Visualizing)
  • Assembly
  • Binning
  • Bin Refinement
• Pathways and Metabolisms of MAGs
  • Before beginning
  • Installing MeaPathways2
  • Installing Pathway Tools
  • Processing MAGs with MetaPathways2 and Pathway Tools
• End-to-End Processing of a Viral Metagenome
  • Downloading the data
  • Read Quality Control
  • Read Quality Control (Visualizing)
  • Assembly
  • Post-Assembly Cleanup?
  • Identifying Viruses
  • Preparing for vConTACT2 and Running vConTACT2

Indices and tables

• Index

• Module Index

• Search Page