All blog posts

How to start a Google VM

Starting a Google VM Sometimes you might want to spin up a Google VM to use: WARNING: There maybe charges for starting a VM, running BigQuery searches, or ...

Searching SRA Metadata in the Cloud

This is another in our series of posts on searching things in the SRA. As we noted previously, NCBI has moved most of the SRA into the clouds, which makes se...

FAME's fabulous ASM tour

A wrap up of the FAME labs’ trip to the Australian Society for Microbiology conference in Sydney

Krona plots are easy (metagenomics example)

Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...

Running AlphaFold on phage lambda

DeepMind’s AlphaFold is winning at predicting tertiary structures from primary amino acid sequences. We thought it would be fun to investigate how it perfo...

NCBI datasets and genome assembly data

Recently, NCBI released their new datasets API that might replace NCBI E-utils. At the moment, datasets is focused on genomes, genes, and viruses, but no dou...

Fast correlations with turbocor

We often want to calculate Pearson correlation between different datasets, for example, we have used it to identify the hosts of different phages. Often, we...

Atavide: importing your data into R

This post is one of a multipart series about analysing your metagenomics samples with Atavide. It is intended to be a quick and dirty look at the superfocus ...

How to install qiime2 on deepthought

Why would I want to do this? I am not really sure, but if you want to use Qiime2 you should install it on deepthought using conda. The sysadmins (may they ...

Snakemake profiles updated

This is an update from a previous post https://fame.flinders.edu.au/blog/2020/09/04/snakemakeprofile where Rob outlines a simple Snakemake profile for runnin...

How to use Snakemake Checkpoints

Snakemake checkpoints are a little complex to get your head around, and so here are two examples that will hopefully clarify some use cases. Before we begin...

Getting started with linux

It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.