What can I do for you? I provide with two different packages of service, one aimed at the management of the bioinformatic side of things in a sequencing facility, the other one at the analysis of NGS or GWAS data to produce publishable results.
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Service 1 – Sequencing facility bioinformatic support
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Typical scenario – You have sequencers (I only support Illumina machines at the moment), you have wet lab facilities, you have a wet lab crew and you have customers that send you genetic material for library preparation and sequencing or they send you library preparations they made themselves for sequencing. So the sequencer, let’s say a HiSeq4000, finishes the run some three to four days later and you have about 0.5 Tb of data onboard from one of the flowcells that needs to be transformed into something meaningful (and hopefully smaller), stored somewhere else and transferred securely to the customer.
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What I provide – I take care of everything from the point that the sequencer has finished the run. The only thing necessary is the hardware that will be connected to the servers and its internet connection. Those costs will be on you, and the amount can vary, but provided with information of the amount and model of sequencers you have I will be able to give you an estimate of the price of the server you would need to run the bioinformatics of the facility. Once purchased I will take care of their installation and administration for as long as I remain providing the service for you.
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Some details – the details of this service, of course, will vary wildly depending on your needs, for which we would need discussion. In general lines I will take care of the data moving from the sequencers to the servers, the demultiplexing of the run’s data into fastq files, the processing of these according to the needs of the facility and/or the customers (e.g. generation of aligned BAM files to a specific version of the reference genome, variant calling from those or annotations and/or prioritizations), the secure transfer of data from the server to the customers and the storage of said data for a period of time.
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Pricing – I charge 50€/hour as a flat tariff for my services, what changes from case to case is the amount of hours per week or month I will invest for each specific case. Depending on the load (number and type of Illumina sequencers) this can range from one to five hours or more per week, with a bigger initial investment of time to set all things running (around ten to twenty hours initially). I will bill you monthly for this services for as long as they are provided.
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Service 2 – Bioinformatics Training
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Typical scenario – You have in your facility a rookie bioinformatician and intend to hire one to take on responsibilities, but don't have anyone with more experience to oversee and guide them in the process.
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What I provide – I will meet with both the supervisor and the potential trainee for an evaluation of the situation, facilities, time investment and capacity. If the project is feasible, I will provide such guidance under the agreed terms (which can vary wildly from situation to situation).
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Pricing – I charge 50€/hour as a flat tariff for my services, what changes from case to case is the amount of hours per week or month I will invest for each specific case. Also much time will it take for the trainee to acquire the desired skills to a satisfactory level will vary significantly and will be dependant on each specific case.
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