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.
Monthly Archives: August 2018
How to mess with BLAST results
Running Mauve with Java 10
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
phage terminase orientation
I was recently looking at the relative orientation of phage terminase genes along the genome. Here is a little summary.
Downloading all the sequences from a PATRIC family
PATRIC families are somehow organized sets proteins that are related. Sometimes we want to get all the protein sequences in the family. Here’s how to do that using the PATRIC command line
Submitting a PATRIC genome annotation using the command line
The PATRIC BRC has a great command line interface that allows you to access much of the data remotely. Here is a simple recipe to submit a genome for annotation.
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