07
Dec
12

User-friendly, open-source personal genome pipeline

Today, GenomeWeb wrote a piece on the STORMSeq pipeline (Scalable Tools for Open source Read Mapping), our newest project in the goal of enabling the public to explore their own personal genetic data. In this pipeline, users upload reads to Amazon S3 and start a webserver in Amazon EC2, where they can set parameters for read mapping and variant calling, all in a graphical user interface. Once they click “GO!”, the pipeline runs and progress and quality control metrics can be monitored, and the final results of the pipeline are uploaded back to Amazon S3. The pipeline itself is free, though the user pays for storage (currently $0.1 per Gb-month) and compute time (currently estimated about $1-2 per exome, $25-35 per genome) on the Amazon cloud. A publication with details about the pipeline is forthcoming, but the pipeline is ready to use now (currently in version 0.8.5) with instructions for use at www.stormseq.org (and the code is available on github.com/konradjk/stormseq).

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