Dirty money: interesting data but unclear what implications are

OK.  So money has microbes on it.  Not surprising.  And when people find out such information they frequently go overboard in the germophobia. See for example these stories from over the years 1999: Filthy Lucre – Paper Money As A Vector Of Disease 2010: Dirty money 1: Expect germs 2010: How Bad Are Germs on Money 2012: …

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 …

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 …

Job: antibiotic resistance in 100k TB genomes

Hi All I’d just like to highlight a job we are advertising, to lead the bioinformatic (sequence+variation) analysis of 100,000 M tuberculosis genomes which we are sequencing (WGS), ~50,000 of which will be phenotyped for 12 drugs, and the remainder for some subset. Note the deadline is very soon – Monday 6th March! This project …

Characterize your metagenomic sequences faster than ever with PALADIN

With our paper recently accepted for publication and many months of practical application, we’re excited to spread the word about our new tool for characterizing metagenomes, PALADIN! Short for Protein ALignment And Detection INterface, PALADIN was our response to the inherent problem of limited references in shotgun metagenomic sequencing. While DNA barcoding involving 16S, 18S, …

Of possible interest – DAS tool for metagenomic binning

Saw an interesting Tweet check out this novel metagenomics tool to reconstruct thousands of high-quality genomes @ChrisMKSieber #banfieldlab https://t.co/67bk8CbFmP — Alexander Probst (@AlexJProbst) February 13, 2017 And this tool may be of interest – it is from a new preprint in BioRXiv.  See abstract below: Microbial communities are critical to ecosystem function. A key objective …

16S rRNA Sequencing Using the Oxford Nanopore Minion

There has been some interest in our recent preprint describing Oxford Nanopore MinIONTM sequencing for 16S rRNA microbiome characterization and I was asked to write a post for microbenet on this technology. Disclaimers – this paper is a work in progress – our paper has not yet been peer-reviewed and we are continuing to revise …

What kind of DNA lingers on ATM keypads? Your food, your skin microbes…and (maybe) parasites

Amidst the November/December holiday chaos, myself and co-authors were proud to witness the publication of a neat new paper focused on ATM keypads in New York City. Yes, just like all other surfaces in the Built Environment, those ATM keypads are harboring lots of microbes and bits of orphaned DNA! This ATM keypad study was work that …

Undergraduate Research Opportunity in Microbiome Informatics at Oregon State University

The Department of Statistics at Oregon State University is hosting a summer REU (Research Experiences for Undergraduates) program that focuses on microbiome data analysis. This is a unique, paid research and training opportunity for STEM undergraduate students who want an interdisciplinary research experience in both biology and statistics. During a ten week training period, students will be …