Everyone should read this piece by Ed Yong: Norm Pace Blew The Door Off The Microbial World

There is a wonderful tribute to Norm Pace in the Atlantic by Ed Yong. Norm Pace truly did blow the door off the microbial world. Source: Norm Pace Blew The Door Off The Microbial World – The Atlantic Lots of good stuff in there about Pace and his career.  See for example this: Pace also …

Could be interesting: The Metagenomics MVP Challenge v1.0

Source: NIST Challenge — CosmosID – Exploring the Universe of Microbes This could be interesting.  NIST & COSMOS ID and ABRF are conducting a metagenomic sequencing methods challenge. From their site: When using metagenomic methods to assess the content of a complex microbial sample, there are many steps in the measurement process where bias might …

WTH is ILR?

WTH is ILR? by Alex Washburne & Jamie Morton Jamie and I have penned a popularization of the isometric log-ratio transform with the intention to allow non-mathematicians to understand the intuition behind what it is, why we use it, and how different methods use the same tool in different ways. The full write-up is available …

Microbiome Bioinformatics with QIIME 2 workshop, June 21-23 2017 in Las Vegas, NV

Members of the QIIME development group, led by Greg Caporaso, will teach a three-day workshop on bioinformatics tools for microbial ecology. The workshop will include lectures covering basic QIIME 2 usage and theory, and hands-on work with QIIME 2 to perform microbiome analysis from raw sequence data through publication-quality statistics and visualizations. This workshop will …

Paper of interest comparing taxonomies of SILVA, RDP, Greengenes, NCBI and OTT 

Just a quick post here.  There is a paper of interest I thought I would call attention to: Source: SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? | BMC Genomics  by Monika Balvočiūtė and Daniel H. Huson Abstract: Background A key step in microbiome sequencing analysis is read assignment to taxonomic units. …

Quick post – this looks potentially very useful – ATLAS – comprehensive infrastructure for assembly, annotation, & genomic binning of metagenomic data 

OK I have not tried this out yet but this could be of interest. ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multi-omics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework …