نبذة مختصرة : International audience ; Antibiotic resistance (ABR) is a major global public health issue designated for urgent action by international institutions, especially regarding the emergence and the global dissemination of multidrug resistant bacteria (MDRB) and antibiotic resistance genes (ARGs) carried by mobile genetic elements. They are widely transmitted between humans, animals, and the environmental domains (One Health context), without borders. Tracking transmissions of outbreaks and identifying sources of contamination is achievable with Whole Genome Sequencing (WGS) data combined with epidemiological information. Ensuring the sharing of high-quality sequence data alongside interoperable curated metadata are key requirements for understanding the spatiotemporal patterns of dissemination of MDRB and ARGs.The ABRomics platform is developed to address such major issues by facilitating systematic bioinformatics analyses for experts working on ABR and the wider research community. Users on the platform can deposit biological sequences, manage projects, and launch various types of analyses to answer generic and specific questions related to AMR. Associated with all deposited sequences, minimal metadata compatible with ENA submission (e.g. ENA prokaryotic pathogen minimal sample checklist: ERC000028) are requested to ensure traceability, and backward and forward compatibility in our data repository.Currently, the platform provides one standardized workflow for the detection of ARGs genes in bacterial genomes. It takes as input genomics WGS sequencing data and does the following analyses: quality checks, genome assembly, taxonomic assignation (species identification), MLST typing (strain identification), plasmid typing and finally detection of ARGs genes and virulence factors. The platform relies on the usegalaxy.fr Galaxy server to perform the bioinformatics analyses allowing complex scientific computation on the IFB Core Cluster. All workflows of the ABRomics project are published on the Intergalactic Workflow ...
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