Next Gen Covid Pathogens Genomics (Congenica)

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    "description": "Technical and Functional Service Requirements* The solution must be capable of accurately processing sequencer output (e.g. BAM/fastq), as well as assembled sequences, and of returning outputs within 4 hours of loading the sequence. * The solution must be capable of incorporating new algorithms into the per-sample sequencing pipeline on a short release cadence to meet evolving public health requirements.* Production and storage of assembled sequence and lineage assignation and variant data is required; these will allow the Authority to detect outbreaks of SARS-CoV-2.* The solution must have options to match a local sequence to global lists of Variants of Concern or other features.* The solution must enable users to upload, analyse and share identifiers necessary to identify genomes.* The solution must be capable of processing at least 100,000 samples a week and be able to ramp up this upwards if required.* A mechanism must exist such that during the upload process, the identifier stored and any other identifiable metadata available to the uploading laboratory (including the laboratory number of the specimen) are provided securely to a secure endpoint designated by the Authority. * The solution must be capable of storing and allowing interrogation of large volumes of processed sequence outputs providing results rapidly. At present, over 1 million sequences have been generated in the UK alone.* The solution must be capable of producing reports in standardised formats as well as generating new reports on an on-demand basis drawing upon information generated in the solution. * Interaction with the system, including data upload, download, querying of stored data, and reporting must be achievable by both fully automated means such as an authenticated REST API, and by interactive web interfaces.* The framework used by the solution must be demonstrably extensible to other pathogens. A plan will be required showing how pipelines processing up to 10 new pathogens could be introduced over the next 12 months using the same framework.* The solution must be able to ingest data from multiple sources including CLIMB-COVID, ENA, GISAID among other sources. The solution must be able to develop interfaces to ingest data from further sources that may be identified in the future. * The solution should allow secure and auditable sequence sharing, if the Authority elects to do so, with defined organisations which may be using the same system. Key Non-Functional Service Requirements* The solution must have a robust support wrapper to ensure continuity of service and the capability for failovers to avoid surveillance blackouts.* There is no requirement for this solution to provide a long-term archive of sequencer output (e.g. BAM/fastq) as part of the solution. By contrast, there is a requirement to store the outputs from analysis of this information.* There is no requirement for the solution to store any patient identifiable data. Samples in the system will be identified by an identifier provided during the upload process.* The solution provider, as data processor, must securely process, store or in transit, all data within the United Kingdom* The solution should be capable of user access management. * A plan must exist for accrediting the solution to ISO15189, ISO17025 or other relevant standards for diagnostic systems* The solution must minimally comply with the following standards: Cyber Security Essentials.",
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