IRIDA contains a number of integrated analysis tools that are able to be launched through the IRIDA web interface. IRIDA’s sample browser and “cart” system allows users to easily select a collection of samples and sequencing data which they want to use in an analysis, then guides users through selecting a pipeline and appropriate parameters for their sample data, and launching their analysis pipeline.
Behind the scenes IRIDA communicates with the Galaxy (https://galaxyproject.org/) workflow system to perform the analysis and track progress of user’s pipelines. When a pipeline is complete, analysis results are transferred back to IRIDA and presented to the user in their browser. A number of pipelines have built in visualization tools for further manual analysis of the results.
Additionally IRIDA records all the information that went into building each analysis result including which input files were used, parameters, and tool versions which can assist in generating reproducible results.
For more information on developing IRIDA workflows see the Development page.
The SNVPhyl (Single Nucleotide Variant PHYLogenomics) pipeline is a pipeline for identifying Single Nucleotide Variants (SNV) within a collection of microbial genomes and constructing a phylogenetic tree. SNVPhyl is able to correctly distinguish outbreak from non-outbreak isolates across a range of variant-calling settings, sequencing-coverage thresholds or in the presence of contamination. SNVPhyl identifies variants and generates a phylogenetic tree by mapping the input sequence reads to a reference genome followed by filtering out any invalid variant calls. The output for the pipeline consists of a whole genome phylogenetic tree constructed from the detected SNVs, as well as a list of all detected SNVs and other information.
More information on SNVPhyl can be found in the SNVPhyl documentation.
Assembly and Annotation
IRIDA’s assembly and annotation pipeline will generate an assembled and annotated genome from reads using FLASH, SPAdes, and Prokka. Outputs produced by this pipeline include: log files, assembly statistics, the contigs (all contigs, filtered contigs with repeats, filtered contigs without repeats), and annotations from Prokka.
IRIDA has integrated the state of the art Salmonella typing tool SISTR. This pipeline rapidly performs simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this pipeline integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST).
Multilocus Sequence Typing (MLST) constructs an ‘allelic profile’ based a limited number of loci from an established MLST scheme. As genomic epidemiology studies strive to gain more detailed strain typing information, these MLST schemes have expanded to incorporate larger portions of the genome. These ‘core genome MLST’ (cgMLST) and ‘whole-genome MLST’ (wgMLST) analyses present a computational challenge.
MentaLiST is an MLST analysis tool, based on a fast k-mer voting algorithm. It is able to make MLST calls directly from raw sequence reads, avoiding a slow assembly stage common to many previous MLST tools. It is specifically designed and implemented to handle large typing schemes.
MentaLiST supports automated downloads of typing schemes from public databases such as pubMLST.org and cgMLST.org.
External Analysis Tools
While IRIDA aims to package and automate many common analysis activities, we understand that researchers may want to use analysis tools that are not included in the IRIDA platform. To enable this IRIDA allows developers to write tools to pull data from the IRIDA system for custom analyses. An example is our IRIDA Galaxy export tool. This allows users to pull data from IRIDA through secure, authenticated channels into their local Galaxy analysis platform to apply any custom workflows and tools they have installed.
IRIDA has also enabled connections with Applied Maths BioNumerics platform, and NCBI’s Sequence Read Archive.
For more information on writing tools to interact with IRIDA, see our [REST API Documentation].
Your pipeline could be included here! IRIDA encourages developers to connect their pipelines to the IRIDA system. See the [Development] page for details.