Galaxy Australia’s 10 millionth job relied on popular locally-developed tool
At any one time, there is a wide array of research being done using Galaxy Australia. When the ten millionth job was submitted to the service recently, it illuminated the importance of good bioinformatics software. The particular job was one of a bunch that analysed various pathogen samples for known antibiotic resistance genes.
Over the last 7 years, more than 40,000 users representing researchers, students, trainers and trainees have demonstrated the platform's versatility across a wide range of fields. This milestone job investigating antimicrobial resistance employed the ABRicate tool, authored by Australian bioinformatician Torsten Seemann. Further investigation showed that 490,507 jobs run on Galaxy Australia also used ABRicate in their workflows!
The University of Melbourne’s A/Prof Torsten Seemann is the Lead Bioinformatician at the Centre for Pathogen Genomics and the Director of Bioinformatics at Doherty Applied Microbial Genomics. As a world-renowned bioinformatician he has developed cutting edge analysis approaches to enhance the use of genomic data. Torsten has authored many popular software tools for the analysis of bacterial sequence data, particularly in the fields of public health and clinical microbiology. He is also a strong advocate for open-source software and open science.
He created ABRicate for the mass screening of assemblies for antimicrobial resistance and virulence genes. Given a FASTA contig file or a genbank file, ABRicate will perform a mass screening of contigs and identify the presence of antibiotic resistance genes. The user can choose which database to search from a list of available antimicrobial resistance databases.
The name ‘ABRicate’ was chosen as the first 3 letters are a common acronym for ‘Anti-Biotic Resistance.’ The word also has the form of an English verb, which suggests the tool is actually taking action against the problem of antibiotic resistance, and it is uniqueit unique enough to be easily searchable.
The tool is widely available to anyone who needs it, and can be found in many repositories. It is one of over 10,000 tools available in the Galaxy Toolshed. There is a tutorial available on the Galaxy Training Network which supports the use of this tool: Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition.
Torsten was recently awarded The Chan Zuckerberg Initiative’s Essential Open Source Software for Science grant for the development of another tool, Snippy. This open-source software tool was written to rapidly identify genetic differences between bacterial genome sequences, and work is underway to allow Snippy to support the latest genome sequencing technologies and viral and fungal pathogens too.
In recognition of the ongoing important contributions that Torsten makes, an award was established in his name. The annual ABABCS ‘Torsten Seemann Outstanding Bioinformatics Software Developer Award’ (previously sponsored by the ARDC) recognises an outstanding EMCR bioinformatic software developer from the Australian community with a view to promoting further efforts to develop and share bioinformatics methodologies.
Are your essential tools available on Galaxy Australia? Request an installation by the Galaxy Australia team if there’s a tool you think should be made available for everyone to use.
Nominate your favourite tool’s author for the Torsten Seemann Outstanding Bioinformatics Software Developer Award.