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 …
New software/tool of possible interest: Source: MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples Software: http://segatalab.cibio.unitn.it/tools/metamlst/ Abstract: Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus …
Quick post. There is a paper out from Jordan Peccia’s lab (authors Karen Dannemiller, Darryl Reeves, Kyle Bibby, Naomichi Yamamoto and Jordan Peccia) of potential interest: Fungal High-throughput Taxonomic Identification tool for use with Next-Generation Sequencing (FHiTINGS) – The paper alas is not open access so I do not have access to it as I write …
Last September, I watched Greg Wilson’s three-minute pitch for Software Carpentry, and I was SOLD! Do I want to get more done at the computer in less time? Absolutely! The only difficulty was waiting until this week for it to happen. Finally, this past Monday and Tuesday (May 13-14,) Software Carpentry arrived at UC Davis. …