Canada's Integrated Rapid Infectious Disease Analysis (IRIDA) platform is designed to equip public health workers and microbiology researchers with easy-to-use tools needed to analyse microbial genomic data - reducing the complexity and technical barriers of traditional tools. IRIDA is free and open-source software. More information is available at www.irida.ca.
This public instance of IRIDA is hosted at Simon Fraser University and managed by the Brinkman lab, as part of the IRIDA consortium. Accounts for evaluating the IRIDA platform on this public instance can be acquired by contacting firstname.lastname@example.org.
Please visit the IRIDA consortium website for more information including an overview of the platform, benefits to using the system, and other highlights. Information for getting started, including several video tutorials, is also available.
Some of the websites for the software below also have links to associated GitHub sites.
|SNVPhyl||Generates a whole genome phylogeny from a set of samples and a reference genome based on single nucleotide polymorphisms (SNVs). Provides a dendrogram, a table of all SNVs used and a SNV distance matrix between each sample.||GitHub|
|SISTR||The Salmonella In Silico Typing Resource (SISTR) generates in silico typing results. It assembles a genome and runs the resulting contigs through https://github.com/peterk87/sistr_cmd/ to generate the final result.||Website|
|MentaLIST||Genotype bacterial samples directly from reads, using an efficient k-mer based algorithm.||GitHub|
|RefSeq Masher||Find what NCBI RefSeq genomes match or are contained in your sequence data.||GitHub|
|IslandViewer||Prediction and visualization of genomic islands. IslandViewer integrates four different genomic island prediction methods: IslandPick, IslandPath-DIMOB, SIGI-HMM, and Islander.||Website|
|GenGIS||Combines digital map data with information about biological sequences.||Website|
|CARD/RGI||Use the Resistance Gene Identifier (RGI) to predict antibiotic resistance genes based on annotations from the Comprehensive Antibiotic Resistance Database.||Website|