SeqSphere+ Software from Ridom allows for automatic processing and analyzing of microbial sequence data obtained from Ion Torrent™ systems. SeqSphere+ Software enables whole genome microbial typing (MLST+) or traditional MLST sequencing projects. This software is designed both for individual labs and for distributed work-groups (client/server model) to enable easy data sharing. License options are available for 1, 3, or 5 years; 2 or 5 seats; and commercial or academic/government labs.
Ridom SeqSphere+ Software Features:
• User-friendly: no scripting skills or bioinformatician needed
• Highly automated workflow: download a pre-designed task template or create a custom template, then apply it to the analysis of hundreds of strains with almost no user intervention.
• Single, expanding nomenclature service: worldwide, unique nomenclature service that enables a ‘Molecular Typing Esperanto’
• DNA re-sequencing editor: edit and analyze reference-mapped assemblies of Ion Torrent™ data (e.g., MLST, MLST+) with auto-correction of homopolymer-related insertion/deletion errors.
• Sanger data: assemble, edit, and analyze Sanger CE sequencing data (e.g., MLST).
• Analytical tools: select data entries from a comparison table for epidemiologic, evolutionary, or functional analysis. Cluster and visualize data entries by using minimum spanning or UPGMA/neighbor-joining trees.
--Store, search, retrieve, export, and create reports from your epidemiologic and DNA sequence data stored in an integrated database. Search new sequence entries against stored data.
--Data fields are compliant with the metadata requirements of the NCBI BioSample. Enables data entry plausibility checks.
• Bacterial typing: typing of bacteria is automatically performed with user-defined quality parameters (e.g., coverage, stop codons) using public or self-defined query libraries and task templates.
• Ridom Community:
--Rapidly and easily share task templates with other institutions or download them online from the Task Template 'Store'.
--Option to contribute to a single, worldwide, expanding, publicly-available database of nomenclature and epidemiologic data. Larger (supra) national institutions may obtain their own server for epidemiologic data upon request.
--Encryption (SSL) of data in transmission
--Various configurable user roles, user groups, and access controls
--Audit trail functionality (who, when and what)
Computer Specifications (Minimum)
Client computer OS: Windows® 7 64-bit, CPU: Core i5, RAM: 8 GB, HD: 500 GB, Internet connection required to use public Ridom MLST+ Nomenclature Server & Task Template 'Store' (supports working with a private and local nomenclature and to generate custom tasks).
Server computer OS: Windows® 7/Linux 64-bit (Ubuntu LTS recommended), CPU: Core i5, RAM: 8 GB (48 GB recommended if MIRA de novo assembly done on this server), HD: 2 TB (RAID level 1 or 5 recommended), it is recommended not to use the NGS machine computer as server.