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 …

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 …

From genomes to phenotypes: Traitar, the microbial trait analyzer

There is an increasing number of studies with a large number genomes recovered from isolate, metagenome, or single cell sequencing. To bridge the gap between the available genome sequences and available phenotype information, we have developed Traitar, a bioinformatics software to phenotype bacteria based on their genome sequence (see workflow below) . Traitar includes phenotype models for …

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 …