Converting a phyloseq object to text files
How to convert a phyloseq object from R to tab-separated values that can be read anywhere
Categories
Blog
Using rclone, teams channels, and onedrive on deepthought
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,...
Extracting some data from Google Cloud
Heres a way to get some PDB files from Google cloud
Searching for metagenomes on the SRA in the cloud
How to search for all the WGS metagenomes in the cloud
Deduplicating a genome assembly
Learn all about deduplicating highly heterozygous genome assemblies
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...
Forking a git repo and then updating the upstream changes
how to update your repo to match code that was added upstream
How to clone a git repository to develop code
a quick set of commands to clone a repository to update code
Accessing NCI resources
Instructions and guidelines for Flinders researchers
Congrats Amber Skye on being awarded first class honours
Congrats to FAME’s first honours student, Amber Skye on her graduation!
FAME's fabulous ASM tour
A wrap up of the FAME labs’ trip to the Australian Society for Microbiology conference in Sydney
How to run a Jupyter notebook on a deepthought node
Most of these instructions come from the official jupyter docs and you should use those as a guide
Congratulations to Laura Inglis
Congrats to FAMEous person - Laura Inglis on her recent achievements!
Meet the Microbiologist podcast
Elizabeth Dinsdale talks Shark Epidermis Microbiomes on American Society for Microbiology podcast.
World Oceans Day 2022
Celebrating World Oceans Days with the Dinsdale Lab research group.
Therapeutic Annotation of Phage Genomes
What should we worry about before we inject phage into people?
Presentations and posters at ASM 2022
View all FAME posters and talks presented at ASM 2022!
Intro to Snakemake Part 2
Yet another Snakemake tutorial, part 2
Celebrating PhD student Susie Grigson’s achievements
Congrats to FAMEous person - Susie Grigson on her recent achievements!
Introduction to Snakemake
Yet another Snakemake tutorial…
Southern eagle ray sampling at Seacliff beach
Southern eagle ray sampling with the Southern Shark Ecology Group (Huveneers lab).
Women’s History Month 1st-31st March
Women’s History month commemorates women’s contribution to history, science, culture, and society.
Happy International Women in Science Day!
On Feb 11th we acknowledge and celebrate the incredible women of STEM on Women in Science Day.
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 ...
Atavide: atavistic metagenome analysis with a vision
A simple pipeline for complex annotations of metagenomes incorporating lots of tools
How to use the VPN to connect to Flinders network
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 ...
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 ...
FAME seed projects for 2021
View project summaries for the FAME seed projects for 2021
How to install and use super-focus on deepthought
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...
How to install and use Kraken2 on deepthought
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...
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...
Rob’s presentation at ASM 2021
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
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.
Managing thousands of files in your Snakemake pipelines
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...
Using PyCharm and Jupyter Notebooks
PyCharm is a terrific Python IDE, and you should use it for code development
How to run a Jupyter notebook on deepthought
Most of these instructions come from the official jupyter docs and you should use those as a guide
Searching the NR database with MMSeqs2
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....
Part 4: Snakemake profiles for DeepThought
Setting up a snakemake profile for deepthought will make your life much easier
Part 3: Using snakemake on deepthought
snakemake is a pipelining tool that allows you to recreate reusable pipelines to analyse data
Part 2: Using conda on deepthought
We are going to use conda to install and update software
Part 1: DeepThought General Overview
Introduction To Using the Flinders HPC ‘DeepThought’ For Bioinformatics
People
Vijini Mallawaarachchi
Research Associate in the Edwards lab
Tina Hauptfeld
Visiting Researcher
Susie Grigson
PhD Student in the Edwards lab
Sarah Giles
Research Associate in the Edwards lab
Ryan Hesse
PhD student in the Dinsdale lab
Robert Constantine
Honours student in the Edwards lab
Rob Edwards
Rob is the Director of Bioinformatics and Human Microbiology for FAME.
Bhavya Papudeshi
PhD student in the Edwards lab
Nick Falk
Research Associate in Microbiome Research in the Dinsdale lab
Michael Roach
Research Fellow in Bioinformatics in the Edwards lab and FAME webmaster
Michael Doane
FAME Liaison and Research Fellow in the Dinsdale lab
Liz Dinsdale
My research uses genomics to investigate the biodiversity and ecology of microbes and viruses on coral reefs, kelp forest and shark epidermis.
Laura Inglis
PhD student in the Edwards lab
Kiarna Taylor
Honours student in the Dinsdale lab
Kale Christopher
Honours student in the Dinsdale lab
Jody McKerral
Research Associate in the Dinsdale lab
Jessica Carlson-Jones
Research Associate in the Edwards lab
Haylee Smith
Honours student in the Dinsdale lab
George Bouras
Visiting Researcher and longtime friend of FAME
Ewan Burns
Honours student in the Dinsdale lab
Evan Pargin
Honours student in the Edwards lab
Emma Kerr
PhD student in the Dinsdale lab
Cong Pham
Honours student in the Edwards lab
Belinda Martin
Research Associate in the Dinsdale lab
Amber Skye
Honours student in the Dinsdale lab and FAME Webmaster
Will Plewa
Undergraduate student in the Edwards lab
Tessa Herewane
Undergraduate student in the Dinsdale lab
Przemysław Decewicz
Visiting Researcher
Sein Hwang
Honours student in the Dinsdale lab
Anal Kanti Roy
PhD student in the Edwards lab
Julie Pederson
Visiting Researcher
Clarice Harker
Honours student in the Edwards lab
Anita Tarasenko
Honours student in the Edwards lab
Abbey Hutton
PhD student in the Edwards lab
Software
Reneo
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...
Trimnami
Trim lots of sequencing reads all at once!
Spae
Phage toolkit to detect and assemble phage candidates for phage therapy.
Snaketool and Nektool
Snaketool and Nektool are frameworks for building command line tools using the Snakemake or Nextflow workflow managers
Phynteny
Phynteny: Synteny-based annotation of bacteriophage genes.
MetaSnek
MetaSnek is a Python package containing miscellaneous functions for metagenomic pipelines!
Koverage
Koverage lets you quickly and easily get coverage statistics from a collection of reads and an assembly.
Atavide
Atavide is a simple, yet complete workflow for metagenomics data analysis!
Pharokka: Fast Phage Annotation Tool
Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
Phables
Phables is a tool developed to resolve bacteriophage genomes using phage bubbles in viral metagenomic data.
Hecatomb
Hecatomb is a pipeline for accurately classifying viral sequences in metagenome samples.
SUPER-FOCUS
SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
Prinseq
PRINSEQ is used for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets.
Phispy
PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes.
PHANOTATE
PHANOTATE is a tool to annotate phage genomes.
FOCUS
FOCUS: An Alignment-Free Model To Identify Organisms In Metagenomes Using Non-Negative Least Squares Usage.
Events
Young Indigenous Women’s STEM Academy
We had the privilege of welcoming CSIRO’s Young Indigenous Women’s STEM Academy to Flinders University for a marine biology workshop.
Women in Science and Engineering
Women in Science and Engineering at Flinders is the newest student club at Flinders University.
Flinders University Marine Biology Association
FAME PhD students Ryan Hesse (President) and Emma Kerr have rebooted FUMBA.
Ocean Science Day
Flinders University marine labs came together to share their love of science during our first annual Ocean Science Day open house.
Bioinformatics workshop in the Democratic Republic of Congo
Bioinformatics workshop
Get Started in Bioinformatics workshop
FAME and COMBINE joint workshop
Cystic Fibrosis Hackathon 2023
Analysing microbiome data from South Australian CF metagenomes
FAME and SAGC Metagenomics Workshop 2022
The second metagenomics workshop hosted by FAME and SAGC took place in July in the Flinders Victoria Square building.
Meeting the respiratory physicians of Alice Springs
In September of 2022, Professor Rob Edwards and Dr. Jess Carlson-Jones visited Alice Springs Hospital to meet with respiratory physicians.
Royal Society of South Australia lecture feat. Liz Dinsdale
Microbiomes of Chondrichthyes: Using basal vertebrates to investigate phylosymbiosis
FAME and SAGC Metagenomics Workshop 2021
The first metagenomics workshop hosted by FAME and SAGC took place in February 2021 at the Tonsley campus at Flinders University.
Adelaide Women in Bioinformatics
The Adelaide Women in Bioinformatics meetup started in 2021 and is now a quarterly meeting.