Advise, please, desktop windows WGS analysis software and R tutorials for all steps from .gb and fasta file processing to reports. Need to do WGS on MDR tuberculosis strains. Tried Ridom SeqSphere, CLC Genomics, R, Geneious pro, Lasergene. Except R, they are all commercial. GATK and SAMtools are not convenient to use fast.
Are you using Galaxy? The public Main Galaxy at http://usegalaxy.org or another site? This forum is for using Galaxy in some way.
There are many tutorials available for Galaxy. Some of the tools in these may be in the Tool Shed, and any tool not found there can be wrapped and added. This wiki has a links to tutorials and usage examples, listed at the very top of the page and in the section "Learning Resources". If you are interested in wrapping a tool, see the right menu with links: Admin and Develop are the places to start.
Thanks, Jen, Galaxy team