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Category Archives: Lab blog
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!
We also provide a snakefile that does all these steps. Set up the bowtie2 index, a directory of reads, and and output location, and it will generate mapped and unmapped reads for you!
Continue readingcrAssphage
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.
Install Anvi’o on an AWS Instance
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.
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