Our paper on the global phylogeography of crAssphage is published in Nature Microbiology. You can read the paper at the Nature Microbiology website or on ReadCube. The paper garnered international press attention, and here we have summarized the press coverage.
Please let Rob know if you are aware of any other reports that are not included here.
For several years NSF ran a trial where they would ask for a conflicts form in excel-type format. Recently, that has been codified into the Collaborators and Other Affiliations Information form. You can find more information about that form at the NSF Website and the NSF GPG.
We developed a simple script to help complete this form for you. It does not do all the work, but it gets you a long way there, and you can do the rest a lot easier. After all, you have a lot of other things to worry about when you are writing that grant. Read more to see how to use it.
We had a great turnout for the 2019 Student Research Symposium as usual, with everyone in the lab either presenting their work or judging the work of others. Congratulations to Dean’s award for Science winners Holly Norman and Ashelyn Lutrick for their presentation on “Analyzing the Presence, in Humans, of crAssphage: A Highly Abundant Bacteriophage Found Around the Globe”.
Here are Jillian, Melisssa, Shane, and Rob in front of Jillian and Shane’s posters.
Our new service, searchSRA provides you with hundreds of bam-format files. However, running the search is only part of the battle, and the next daunting step is the downstream processing. Here are some hints about processing the data.
AKA: how to remove contamination from your metagenome! We use sharks genomes, but it works with humans, corals, and other things too!
A while ago we wrote deconseq to allow you to remove contamination from your sequence libraries. We used an HTS-mapper to map the reads in your sequences to your reference genome, and then filtered the sequences after mapping.
This is trivial to do with modern sequence analysis tools, and so we provide recipes here for filtering your reads based on matches to a reference genome. Read more to find out how!
The NCBI SRA contains a lot of data – about 1016 bp at the moment! However, searching that has always been problematic. We’re happy to unveil a new search SRA service that allows you to search the random metagenomes in the SRA using either DNA or protein queries.
We are pleased to announce the second installment of the SoCal Bioinformatics Hackathon.
From 9-11 January, 2019, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University! We are going to put a few hundred thousand metagenomic datasets on cloud infrastructure and identify known, taxonomically definable and novel viruses! We’re specifically looking for folks who have experience in Computational Virus Hunting or Adjacent Fields! If this describes you, please apply! This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for virological analyses from high-throughput experiments. The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).