Software Development

The following open source projects have had significant input into their design and implementation from our experts (nb. attribution will sometimes refer to legacy name of VLSCI):

Annokey. Gene-based search for key-terms in the NCBI gene database and associated PubMed abstracts. bjpop.github.io/annokey/. Published in Source Code for Biology and Medicine, 2014. www.scfbm.org/content/9/1/15. Collaboration with the GEL lab, Department of Pathology, University of Melbourne.

Bpipe. A bioinformatics pipeline. github.com/ssadedin/bpipe. Published in Bioinformatics 2012. bioinformatics.oxfordjournals.org/content/early/2012/04/11/bioinformatics.bts167.abstract. Collaboration with Murdoch Children’s Research Institute.

Cpipe, a shared variant detection pipeline designed for diagnostic settings, published in Genome Medicine: genomemedicine.biomedcentral.com/articles/10.1186/s13073-015-0191-x.

Degust. A web tool to help analyse, visualise and fully appreciate Differential Gene Expression data from RNA-seq experiments. www.vicbioinformatics.com/software.degust.shtml. Collaboration with VBC, Monash University.

FAVR. Filtering and Annotation of Variants that are Rare. github.com/bjpop/favr. Published in BMC Bioinformatics, 2013. www.biomedcentral.com/1471-2105/14/65/abstract.  Collaboration with the GEL lab, Department of Pathology, University of Melbourne.

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud. Published in PLOS ONE: journals.plos.org/plosone/article?id=10.1371/journal.pone.0140829.

Hi-Plex. A streamlined highly-multiplexed PCR-based target-enrichment system for massively parallel sequencing suitable for an extensive range of clinical and research applications. Hi-Plex is complemented by software for primer design and variant calling. The Hi-Plex tool and workflow (April 2015) Paper “Abridged adapter primers increase the target scope of Hi-Plex” is listed in Top Ten Biotechniques Peer reviewed papers for 2015.

HiTIME. High-resolution Twin-Ion Metabolic Extraction. github.com/bjpop/HiTIME. Collaboration with Department of Chemistry, UoM. Published in Analytical Chemistry: High-Resolution Twin-Ion Metabolite Extraction (HiTIME) Mass Spectrometry: Nontargeted Detection of Unknown Drug Metabolites by Isotope Labeling, Liquid Chromatography Mass Spectrometry, and Automated High-Performance Computing pubs.acs.org/doi/abs/10.1021/ac504767d.

Methpat. A program for summarising CpG methylation patterns. github.com/bjpop/methpat. Collaboration with the Ludwig Institute for Cancer Research. Published in Gigascience: Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat. gigascience.biomedcentral.com/articles/10.1186/s13742-015-0098-x

Methpat in the news, 26/6/2016

Prokka. A software tool for the rapid annotation of prokaryotic genomes. www.vicbioinformatics.com/software.prokka.shtml. Published in Bioinformatics, 2014. In collaboration with VBC, Monash University. This high-profile software has reached 374 citations in less than two years. Version 1.12 released 14 March 2017.

Rover. Read-pair overlap considerate variant-calling software for PCR-based massively parallel sequencing datasets. github.com/bjpop/rover. Published in Source Code for Biology and Medicine, 2014. www.scfbm.org/content/9/1/3. Collaboration with the GEL lab, Pathology, University of Melbourne. Part of the Hi-Plex project: www.hiplex.org/ Simple, low-cost, modular targeted DNA sequencing technology. Supported by NHMRC project grant APP 1025879.

Rubra. A bioinformatics pipeline. github.com/bjpop/rubra. Presented at the Bioinformatics Open Source Conference, 2013 (BOSC2013). Used by many bioinformatics projects at Melbourne Bioinformatics.

SRST2. Short Read Sequence Typing for Bacterial Pathogen. github.com/katholt/srst2. Accepted for publication in Genome Medicine, 2014. Collaboration with University of Melbourne scientists Assoc Prof Kat Holt and Dr Mike Inouye.

BioMedCentral Announcement re SRST2, 18/12/2014

Kat Holt’s blog announcement re SRST2, 26/11/2014

UNDRROVER. A fast and accurate DNA mutation detector for targeted DNA sequencing. github.com/bjpop/undr_rover. Published in BMC Bioinformatics. Created by Melbourne Bioinformatics experts Assoc Prof Daniel J. Park, Mr Roger Li, Mr Edmund Lau, Mr Peter Georgeson, Dr Tú Nguyen-Dumont and Dr Bernard J. Pope.

The following list is a selection of popular software developed by bioinformaticians working by our Microbial Genomics experts:

Over 50 ‘recipes’ for Homebrew Science to make it easy for people to install bioinformatics software have been published by our experts.