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Case Study: Taking delivery of millions of sequences
GenomeQuest provides access to annotated next-generation sequence data for immediate analysis by researchers
Research groups pursuing genome- and metagenome-scale investigations often face the significant technical issue of how to receive a data set consisting of millions of sequences. This problem is significant because the data itself does little to advance the process of an investigation. It must be received into an environment that enables access, analysis, sorting, and visualization.
Sequencing service facilities engaged to produce large sequencing data sets usually deliver the data as a long text file with the sequences in a standard format such as FASTA. Without appropriate bioinformatics resources in place, initial annotation and evaluation of the data contained by the file can take up to a year's worth of attention and close evaluation by a team of bioinformaticists and IT personnel.
In a consulting project performed on behalf of a contract sequencing facility, GenomeQuest's consulting service organization leveraged the power of the GenomeQuest platform to provide a solution that enabled the facility's customers to begin sequence data analysis, and realize value from the new data, immediately upon delivery.
Following QA analysis of the entire set,(Read Case Study: Next-Generation QA for a Next-Generation Sequencing Service Facility) each of the new sequences was annotated by adding the annotation of the best hit from the public databases to its record. The annotated sequences were then added as a database to a secure GenomeQuest account.
By providing their customer with access to the account, the sequencing service facility effectively completed delivery of the annotated sequence data they were contracted to provide. Furthermore, their customer received the data within the powerful and familiar GenomeQuest environment. The data can be accessed by the customer via GenomeQuest's web-browser interface, and analyzed and visualized in GenomeQuest. Because first-pass annotation has already been performed, the customers can easily locate sequences of interest within the new data, in addition to doing identity and similarity comparisons between the new sequences and the sequences comprising databases such as GenBank, GQ-PAT, and DrugBank PRO.