JGI Microbial Genetics and Metagenomics Workshop

I recently came back from JGI’s Microbial Genomics and Metagenomics workshop and wanted to blog about it.  The workshop’s purpose was focused on teaching scientists how to use IMG Data Management and Analysis Systems.  For the penny counters, the registration fee was $350 and they reserve hotel rooms at government rate of $101/night.  The workshop was five days long and was composed of hands on tutorials mixed with scientific talks.  Overall, I thought this was a pretty good workshop, however, I was frustrated with the fact that unless you have assembled data, 454 data, or collaborate with JGI, you are unable use IMG.  To me, assembly is a big part of analyzing datasets.  There are many programs to use, different kmer sizes, and it depends on what kind of dataset you have.  In my case, I have mainly datasets composed of 16S rDNA and assembly is quite difficult. Nevertheless, there are some amazing features IMG has.  First, IMG database is free available to anyone.  One of the perks of working with the JGI is that they require the researcher to make the datasets publicly available.  Anyone can make an account with IMG and span through the thousands of genomes, metagenomes, and transcriptomes online.  The workshops has tutorials for almost every part of IMG (IMG, IMG-M, IMG-ER, IMG-MER, IMG-HMP).  Now, the tutorials go quite fast and you cannot access IMG when the tutorial is going on because the system will slow down but IMG is quite user friendly.  I was recently scanning my notes using IMG and I found if I just browse around I can eventually get when I wanted to go.  In all IMG has tools that can compare genomes, find genes of interest, find a function of interest (KEGG, COG, Pfam, etc), and compare genomes (dot plots, distance trees, compare function).

What does IMG offer? (shortcut version)
IMG – where the databases are. If you do not have an account, you can still use this part of IMG.  Whole genomes from the three domains of life are available as well as plasmids and gene fragments.   You can sort based on metadata available however, as a warning some users did not upload all the metadata.  You can use the IMG tools to find particular genes of interest or compare genomes, find functions.

IMG-ER – This is just like IMG except you can use all the IMG tools on your own dataset. And you can perform annotations.  

IMG-M – Same as IMG but now includes metagenomes.

IMG-MER – Same as IMG-M but now you can analyze your own metagenomes.

IMG-HMP – Same as IMG but contains datasets from the Human Microbiome Project metagenomes

All in all, IMG has some really nice tools to use.  I will definitely start using IMG with my own dataset.  My only concern is using their tools for unassembled datasets.  JGI is moving IMG towards allowing for this for non-collaborators and hopefully will have this available to everyone in the near future.

 

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