We have been working on updating access to the SRA metadata. In previous posts, we used the SQLite database provided by the Meltzer lab, but for a variety of reasons, we are now using the XML provided by the NCBI.
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Category Archives: Lab blog
Press about Global Phylogeography of crAssphage
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.
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NSF Collaborators and Other Affiliations Information
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.
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Counting K-mers
One of the most essential tools in bioinformatics is counting k-mers. These are short, identical strings, of length k. Here, we will look at counting all the k-mers in string.
Edwards Lab @ SRS
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.
Search SRA Data
Our new service,
command line deconseq
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
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!
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crAssphage
We have a series of posts about crAssphage. Enjoy them!
Similarity Searching the SRA
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.
Phage Gene Callers
Which phage gene callers are people using?
We are curious how people annotate their phage genomes, and so we looked at both the genbank records and the literature.