Sarah Giles
Research Associate in the Edwards lab
Research Associate in the Edwards lab
Honours student in the Edwards lab
Research Fellow in Bioinformatics in the Edwards lab and FAME Webmaster
Honours student in the Dinsdale lab
Honours student in the Dinsdale lab
Research Associate in the Dinsdale lab
Research Associate in the Edwards lab
Honours student in the Dinsdale lab
Honours student in the Dinsdale lab
Honours student in the Edwards lab
Honours student in the Edwards lab
Honours student in the Dinsdale lab and FAME Webmaster
Undergraduate student in the Edwards lab
Undergraduate student in the Dinsdale lab
PhD student in the Edwards lab
PhD student in the Dinsdale lab
PhD student in the Edwards lab
PhD student in the Edwards lab
PhD student in the Dinsdale lab
Undergraduate student in the Dinsdale lab
Honours student in the Dinsdale lab
Honours student in the Edwards lab
PhD student in the Edwards lab
PhD student in the Edwards lab
This blog post covers how to set up an R environment to run on a deepthought node. This is useful if you have analysis to do in R that requires too much memo...
Most of these instructions come from the official jupyter docs and you should use those as a guide
It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.
PyCharm is a terrific Python IDE, and you should use it for code development
Most of these instructions come from the official jupyter docs and you should use those as a guide
Setting up a snakemake profile for deepthought will make your life much easier
snakemake is a pipelining tool that allows you to recreate reusable pipelines to analyse data
We are going to use conda to install and update software
Introduction To Using the Flinders HPC ‘DeepThought’ For Bioinformatics
This blog post covers how to set up an R environment to run on a deepthought node. This is useful if you have analysis to do in R that requires too much memo...
Most of these instructions come from the official jupyter docs and you should use those as a guide
Most of these instructions come from the official jupyter docs and you should use those as a guide
Setting up a snakemake profile for deepthought will make your life much easier
snakemake is a pipelining tool that allows you to recreate reusable pipelines to analyse data
We are going to use conda to install and update software
Introduction To Using the Flinders HPC ‘DeepThought’ For Bioinformatics
Snaketool and Nektool are frameworks for building command line tools using the Snakemake or Nextflow workflow managers
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...
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...
Hecatomb is a pipeline for accurately classifying viral sequences in metagenome samples.
I’m working on a pipeline that uses and generates tens of thousands of files, and there’s a good chance this could be expanded to produce hundreds of thousa...
Setting up a snakemake profile for deepthought will make your life much easier
snakemake is a pipelining tool that allows you to recreate reusable pipelines to analyse data
Trim lots of sequencing reads all at once!
Phage toolkit to detect and assemble phage candidates for phage therapy.
Snaketool and Nektool are frameworks for building command line tools using the Snakemake or Nextflow workflow managers
MetaSnek is a Python package containing miscellaneous functions for metagenomic pipelines!
Koverage lets you quickly and easily get coverage statistics from a collection of reads and an assembly.
Atavide is a simple, yet complete workflow for metagenomics data analysis!
Hecatomb is a pipeline for accurately classifying viral sequences in metagenome samples.
Trim lots of sequencing reads all at once!
Phage toolkit to detect and assemble phage candidates for phage therapy.
MetaSnek is a Python package containing miscellaneous functions for metagenomic pipelines!
Koverage lets you quickly and easily get coverage statistics from a collection of reads and an assembly.
Atavide is a simple, yet complete workflow for metagenomics data analysis!
Visiting Researcher
Visiting Researcher and longtime friend of FAME
Visiting Researcher
Visiting Researcher
Research Associate in Bioinformatics in the Edwards lab and FAME Webmaster
Research Associate in Microbiome Research in the Dinsdale lab
FAME Liaison and Research Fellow in the Dinsdale lab
Research Associate in the Dinsdale lab
Phables is a tool developed to resolve bacteriophage genomes using phage bubbles in viral metagenomic data.
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes.
PHANOTATE is a tool to annotate phage genomes.
Analysing microbiome data from South Australian CF metagenomes
The second metagenomics workshop hosted by FAME and SAGC took place in July in the Flinders Victoria Square building.
In September of 2022, Professor Rob Edwards and Dr. Jess Carlson-Jones visited Alice Springs Hospital to meet with respiratory physicians.
The first metagenomics workshop hosted by FAME and SAGC took place in February 2021 at the Tonsley campus at Flinders University.
This blog post covers how to set up an R environment to run on a deepthought node. This is useful if you have analysis to do in R that requires too much memo...
Most of these instructions come from the official jupyter docs and you should use those as a guide
PyCharm is a terrific Python IDE, and you should use it for code development
Most of these instructions come from the official jupyter docs and you should use those as a guide
FAME lab at Viruses of Microbes Meeting, Cairns 2024
A wrap up of the FAME labs’ trip to the Australian Society for Microbiology conference in Sydney
View all FAME posters and talks presented at ASM 2022!
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
MetaSnek is a Python package containing miscellaneous functions for metagenomic pipelines!
Atavide is a simple, yet complete workflow for metagenomics data analysis!
How to search for all the WGS metagenomes in the cloud
A simple pipeline for complex annotations of metagenomes incorporating lots of tools
Global Phage Host Prediction Consortium White Paper Robert Edwards, Flinders University September 2023 For comment Please contact Rob Edwards (robert.edward...
Phynteny: Synteny-based annotation of bacteriophage genes.
What should we worry about before we inject phage into people?
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...
Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...
SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
FOCUS: An Alignment-Free Model To Identify Organisms In Metagenomes Using Non-Negative Least Squares Usage.
Recently, our HPC, deepthought has been running low on storage space. There are several options, but one that we are using is to combine deepthought, rclone,...
super-FOCUS Super-FOCUS is a tool to identify the functions that the sequences in your metagenome are doing. As a benefit, it also identifies the taxonomy a...
Kraken2 Kraken2 is a tool to identify the taxonomy of the things in your environmental sample. It does not identify what those things are doing, but what is...
Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
What should we worry about before we inject phage into people?
A simple pipeline for complex annotations of metagenomes incorporating lots of tools
It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.
We are going to use conda to install and update software
Matthew Flinders Fellow in Bioinformatics
Matthew Flinders Fellow in Marine Biology
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
Hecatomb is a pipeline for accurately classifying viral sequences in metagenome samples.
How to convert a phyloseq object from R to tab-separated values that can be read anywhere
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 ...
Heres a way to get some PDB files from Google cloud
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...
FAME lab at Viruses of Microbes Meeting, Cairns 2024
A wrap up of the FAME labs’ trip to the Australian Society for Microbiology conference in Sydney
how to update your repo to match code that was added upstream
a quick set of commands to clone a repository to update code
Heres a way to get some PDB files from Google cloud
How to search for all the WGS metagenomes in the cloud
Heres a way to get some PDB files from Google cloud
How to search for all the WGS metagenomes in the cloud
We have a computational problem searching the Non-Redundant database, but we can solve that! If you use MMSeqs2 to search the NR database, it needs about 1....
We have a computational problem searching the Non-Redundant database, but we can solve that! If you use MMSeqs2 to search the NR database, it needs about 1....
We have a computational problem searching the Non-Redundant database, but we can solve that! If you use MMSeqs2 to search the NR database, it needs about 1....
We have a computational problem searching the Non-Redundant database, but we can solve that! If you use MMSeqs2 to search the NR database, it needs about 1....
We have a computational problem searching the Non-Redundant database, but we can solve that! If you use MMSeqs2 to search the NR database, it needs about 1....
PRINSEQ is used for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets.
PyCharm is a terrific Python IDE, and you should use it for code development
Hecatomb is a pipeline for accurately classifying viral sequences in metagenome samples.
It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
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...
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...
Kraken2 Kraken2 is a tool to identify the taxonomy of the things in your environmental sample. It does not identify what those things are doing, but what is...
super-FOCUS Super-FOCUS is a tool to identify the functions that the sequences in your metagenome are doing. As a benefit, it also identifies the taxonomy a...
super-FOCUS Super-FOCUS is a tool to identify the functions that the sequences in your metagenome are doing. As a benefit, it also identifies the taxonomy a...
View project summaries for the FAME seed projects for 2021
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 ...
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 ...
Why would I want to connect to the network. When you connect to the VPN it makes it seem like you are on the Flinders University Network even if you are at ...
Why would I want to connect to the network. When you connect to the VPN it makes it seem like you are on the Flinders University Network even if you are at ...
Why would I want to connect to the network. When you connect to the VPN it makes it seem like you are on the Flinders University Network even if you are at ...
A simple pipeline for complex annotations of metagenomes incorporating lots of tools
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 ...
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...
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...
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...
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...
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...
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...
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...
Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...
Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...
What should we worry about before we inject phage into people?
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...
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 ...
How to search for all the WGS metagenomes in the cloud
Heres a way to get some PDB files from Google cloud
FAME and COMBINE joint workshop
Recently, our HPC, deepthought has been running low on storage space. There are several options, but one that we are using is to combine deepthought, rclone,...
Recently, our HPC, deepthought has been running low on storage space. There are several options, but one that we are using is to combine deepthought, rclone,...
Recently, our HPC, deepthought has been running low on storage space. There are several options, but one that we are using is to combine deepthought, rclone,...
Recently, our HPC, deepthought has been running low on storage space. There are several options, but one that we are using is to combine deepthought, rclone,...
Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
Koverage lets you quickly and easily get coverage statistics from a collection of reads and an assembly.
Phynteny: Synteny-based annotation of bacteriophage genes.
Phage toolkit to detect and assemble phage candidates for phage therapy.
Phage toolkit to detect and assemble phage candidates for phage therapy.
Trim lots of sequencing reads all at once!
Trim lots of sequencing reads all at once!
Trim lots of sequencing reads all at once!
How to convert a phyloseq object from R to tab-separated values that can be read anywhere
How to convert a phyloseq object from R to tab-separated values that can be read anywhere
How to convert a phyloseq object from R to tab-separated values that can be read anywhere
Reneo means to unravel or untangle in Latin. Reneo is a software developed to unravel or untangle high-quality genomes from viral communities (including both...
Reneo means to unravel or untangle in Latin. Reneo is a software developed to unravel or untangle high-quality genomes from viral communities (including both...
Global Phage Host Prediction Consortium White Paper Robert Edwards, Flinders University September 2023 For comment Please contact Rob Edwards (robert.edward...
Global Phage Host Prediction Consortium White Paper Robert Edwards, Flinders University September 2023 For comment Please contact Rob Edwards (robert.edward...
Global Phage Host Prediction Consortium White Paper Robert Edwards, Flinders University September 2023 For comment Please contact Rob Edwards (robert.edward...
Paparazzi spotted FAMEous researchers at Australian Society of Microbiology in Brisbane. Professor Dinsdale chaired the shark infested Environmental Microbes...
Paparazzi spotted FAMEous researchers at Australian Society of Microbiology in Brisbane. Professor Dinsdale chaired the shark infested Environmental Microbes...