rwmurdoch / utk-mgrast

UTK-MGRAST

Schedule

Repository for a day-and-a-half workshop on using MG-RAST for metagenomics to be held at University of Tennessee Knoxville March 15-16 2018.

Your instructors are Robert Murdoch, Coordinator for the Center for Biotechnology at UTK and Will Trimble from Argonne National Laboratory

There is an etherpad group chat room for this class-- feel free to ask questions or take notes here. It's world readable and world writeable.

Thursday, March 15, 2018

• Things you should know about cloud computing

• Sequences, computing, MG-RAST and you

• MG-RAST website walkthrough

• Sequencing core horror stories

• Lunch

• MG-RAST API--introducing the firehose

• Sequencing-by-synthesis videos and code

Friday, March 16, 2018

• MG-RAST Tools (using docker)

• Using the NCBI API (using docker)

• open shop

Additional resources

Resources on Cloud computing and bioinformatics

• Argonne soils automation workshop 2014 This workshop had a more expansive day-and-a-half workshop in 2014.
• ANGUS Next-Gen Sequence Analysis Workshop 2017 An amazing, cloud-based set of tutorials for beginners in NGS sequence analysis
• EDAMAME course Tutorial on 16S sequence analysis using QIIME (and R)
• Adina's NCBI lesson--building a private BLAST database

Resources on the Shell

• Software Carpentry reference page
• Software Carpentry tutorial - The Unix shell
• The shell handout (pdf)- Command Reference
• explainshell.com
• Intro to Bash Programming

Links for MG-RAST

• MG-RAST
• MG-RAST API explorer
• MG-RAST Search API explorer
• MG-RAST user manual
• MG-RAST's code
• Skyport--MG-RAST's workflow management