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,
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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We have a series of posts about crAssphage. Enjoy them!
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 curious how people annotate their phage genomes, and so we looked at both the genbank records and the literature.
We wanted to use Anvi’o on a windows machine, but that is impossible, so we set up an AWS free instance with anvi’o 5 up and running for the windows users. Here’s how to do it.
They short answer is you can’t (currently) run the totally awesome Mauve with Java 10, but you can probably run Mauve anyway. Here’s how!
TL;DR
locate java | grep java$ | grep -w bin export JAVA_CMD=/usr/lib/jvm/java-8-openjdk-amd64/bin/java
I was recently looking at the relative orientation of phage terminase genes along the genome. Here is a little summary.