Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service

Abstract

Background Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily actionable by researchers through convenient access points and supported by adequate IT infrastructures. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of “on-demand” Galaxy instances over the cloud. By facilitating the set-up and configuration of Galaxy web servers, Laniakea provides researchers with a powerful and highly customisable platform for executing complex bioinformatics analyses. The system can be accessed through a dedicated and user-friendly web interface that allows the Galaxy web server’s initial configuration and deployment. Results “Laniakea@ReCaS”, the first instance of a Laniakea-based service, is managed by ELIXIR-IT and was officially launched in February 2020, after about one year of development and testing that involved several users. Researchers can request access to Laniakea@ReCaS through an open-ended call for use-cases. Ten project proposals have been accepted since then, totalling 18 Galaxy on-demand virtual servers that employ ~ 100 CPUs, ~ 250 GB of RAM and ~ 5 TB of storage and serve several different communities and purposes. Herein, we present eight use cases demonstrating the versatility of the platform. Conclusions During this first year of activity, the Laniakea-based service emerged as a flexible platform that facilitated the rapid development of bioinformatics tools, the efficient delivery of training activities, and the provision of public bioinformatics services in different settings, including food safety and clinical research. Laniakea@ReCaS provides a proof of concept of how enabling access to appropriate, reliable IT resources and ready-to-use bioinformatics tools can considerably streamline researchers’ work.

Detection and Characterization of Zoonotic Pathogens in Game Meat Hunted in Northwestern Italy

“…While HEV testing is typically performed in the liver, we tested the muscle tissue because it is more suitable from a food safety perspective. Furthermore, previous studies conducted in Italy reported a prevalence of 1.35% and 5.6% in wild boar muscle [18] and muscle and liver [33], respectively.…”

“…Bioinformatic analysis was performed using the Galaxy interface [32,33]. The raw reads were trimmed using Trimmomatic 0.38 [34] for removing Nextera adaptors and other Illumina-specific sequences (Illuminaclip set to Nextera (paired-ended)), removing low-quality residues at the start and the end of the reads (leading:10 and trailing:10), clipping reads when the average Q-scores dropped below 20 over a sliding window of four residues (sliding window, 4:20), and dropping reads shorter than 40 bases after processing (minlen, 40).…”

First Report of Food Poisoning Due to Staphylococcal Enterotoxin Type B in Döner Kebab (Italy)

“…All the bioinformatic analyses were performed using the tools on the Staphylococcus aureus Intensive Server for Research in Omics data (SIRIO) Galaxy instance ( accessed on 1 August 2023): an online user-friendly Galaxy interface for performing raw read trimming, assembly, and SE gene detection [ 30 , 31 ]. The raw reads were trimmed using Trimmomatic 0.38 [ 32 ] by removing the Nextera adaptors and other Illumina-specific sequences (Illuminaclip set to Nextera (paired-ended)), by removing low-quality residues at the start and the end of the reads (leading:10 and trailing:10), by clipping the reads when the average Q-scores dropped below 20 over a sliding window of four residues (slidingwindow:4:20), and by dropping the reads shorter than 40 bases after processing (minlen:40).…”

A Case of Food-Borne Salmonellosis in a Corn Snake (Pantherophis guttatus) after a Feeder Mouse Meal

“…All bioinformatic analyses were performed with the tools on the Galaxy instance S.I.R.IO. http://90.147.102.165/galaxy, an online user-friendly Galaxy interface for performing bacterial genome analyses [28][29][30]. The raw reads were trimmed using Trimmomatic 0.38, by removing Nextera adaptors and other Illumina-specific sequences (Illuminaclip set to Nextera, paired-ended), by removing low-quality residues at the start and the end of the reads (leading:10 and trailing:10), by clipping reads when the average Q-scores dropped below 20 over a sliding window of four residues (slidingwindow:4:20) and by dropping reads shorter than 40 bases after processing (minlen:40) [31].…”