tealfurnholm/strain-level_metagenome_analysis

Using a universal reference database, mixed assemblies, and cutting-edge software to give you the quantitative community phylogeny, a complete community functional analysis, and many strain(ish)-level high-quality bins.

OVERVIEW

• The tail-end of the pipeline - binning and secondary analysis - are being worked on as of 5/17/21. This message will disappear once it is complete.

This pipeline is for paired short-read metagenome analysis.

It uses a "universal database" and novel in-house scripts to create strain-level bins, as well as doing comprehensive linked community+functional primary and secondary gene analyses. This pipeline analyses each sample separately, but there is a co-assembly option, and the binning process can be run with multiple samples.

Requirements

• You should be doing this in a unix/linux shell environment
• I usually use a max of 40 threads (excep the perl scripts only use 1)
• You'll want/need a few hundred GB of RAM
• If you don't already have them on your system, install perl and make sure it can run from any folder: https://www.perl.org/get.html
• The wiki will help you download and place any additional software.

Start Here