Metagenomics - Chris Quince

Chris Quince has provided a lovely metagenomics tutorial that uses a custom VM. The tutorial covers analysis of a shotgun metagenomics dataset and includes demonstrations of taxonomic profiling, functional profiling, metagenomics assembly and genome reconstruction.

Software used: Metaphlan2, bwa, samtools, CONCOCT, megahit, prodigal, parallel, blast, COG RPS database, GFF python.

The tutorial can be found here:

How are we supposed to get started on this? Seems to be a continuation of something previous. There is no “Projects” directory on the standard VM offering?!

Still no projects directory on the standard VM.

Also no metagenomics image to load from :frowning: @chrisq0 @nickloman

Hi, I have alot of metagenomic data and would like to go through the procedures in your tutorial. Im still unsure where the origonal data is. The tutorial also referes to a custom R scritpt, are these all available on an instance ( wich i cant find) or is there a download.

any help much apreciated


Hi Garry - I’m looking into this.

I think we took some of the images from the CLIMB launch down, but I’ll try and sort out some way of making all of the materials available permanently.

More info to follow…

Any progress on this yet?

Hi Rob, I am making progress on this - will update once I’m done.

I am also very keen to go through this tutorial and it would be very helpful if we could have access to the material - if so can you let me know how to do this (can’t find downloadable files in the tutorial link)?

The last post on this thread was 12 months ago, and the tutorial is now almost two years old (and has never worked particularly well!).

We will look to provide an updated metagenomics tutorial, likely based on Chris Quince’s metagenomics workshop: