Microbial community, microbiome, and metagenomic analysis tools of the week

Compiling some of the more interesting tools I have seen recently. Some I have plyed with but most I have just looked at the papers briefly.

Microbiome | Abstract | VizBin – an application for reference-independent visualization and human-augmented binning of metagenomic data.

Global biogeographic sampling of bacterial secondary metabolism

GrammR: Graphical Representation and Modeling of Count Data with Application in Metagenomics

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data

Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking

Phylogenetics and the human microbiome

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.