Software Development

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

ABRicate. Mass screening of contigs for antimicrobial and virulence genes. github.com/tseemann/abricate

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

MLST. For scanning contig files against PubMLST typing schemes. github.com/tseemann/mlst.

Nullabor. Pipeline to generate complete public health microbiology reports from sequenced isolates. github.com/tseemann/nullabor.

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.

Snippy. Rapid haploid variant calling and core SNP phylogeny. github.com/tseemann/snippy.

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.

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