Description of the contract
Introduction
The University of Bristol is seeking a single provider to support a number of large research projects for which the research group undertakes surveillance of bacterial isolates from a variety of human and animal sources in the UK, Argentina and Thailand.
The research is funded by for Arwain DGC (Defnydd Gwrthfioteg Cyfrifol / Leading on the responsible use of antimicrobials Wales); and the UKRI Biotechnology and Biological Sciences Research Council (BBSRC).
The contract must be in place during December 2022.
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General Requirements
In order to fully characterise the genomes of Gram negative bacterial isolates for a variety of research projects, we require a bacterial whole genome sequencing specialist service on an Illumina platform generating 2x250bp paired-end reads at a minimum depth of coverage of 30x and a median insert sizes greater than 600bp.
The bacteria under study are known to lose plasmids in cold storage conditions over time. In order to mitigate against plasmid loss we need a sequencing provider who has existing protocols that preserve the DNA of the isolates as close to the point of isolation as possible.
For each isolate we can provide the equivalent of 8 OD600nm or 4 x 109 cells.
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Commissioning of Work
The isolates are currently prepared in batches of 93 with the requirement to ship the order in multiple batches. The volume of work will fluctuate dependant on the research project outputs.
Orders will normally be placed via a University of Bristol Purchase Order, covering the batch work over a period of time.
Batches are currently posted to the supplier by the University at the University’s expense.
Bidders should confirm batch requirements if different to 93 and any shipping protocols.
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Data Requirements
These data sets are key to a number of large research projects and we require data to be cross-comparable between projects. Therefore, for these projects we also require several bioinformatics services, including taxonomic assignment using Kraken, mapping, variant calling, assembly and annotation (fasta, gbk, gff, fastq files).
We will require the data to be generated and the bioinformatics completed for each batch of isolates within 8 weeks of receipt of the isolates.
Data should remain available for access from the provider for a minimum of 12 months from the date of sequencing completion and be provided on a centralised platform rather than only via data link.
Bidders should describe how the data is stored, released and accessed by the University.
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