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).
- Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples. Kosmicki JA, Samocha KE, Howrigan DP, Sanders SJ, Slowikowski K, Lek M, Karczewski KJ, Cutler DJ, Devlin B, Roeder K, Buxbaum JD, Neale BM, MacArthur DG, Wall DP, Robinson EB, Daly MJ
- You want a VCF? You got it. 6 hours ago
- RT @matei_zaharia: Learn how the Broad Institute used #ApacheSpark for genomics! My favorite talk from Spark Summit East. https://t.co/3yLo… 1 week ago
- RT @skathire: That feeling when the usual Friday 4PM conference call is cancelled. https://t.co/cQNOQWKdqe 2 weeks ago
- RT @ryanlcollins13: @dgmacarthur I'm starting to think that 2016/2017 may actually be a secretly disguised EDx course on Bayesian probabili… 3 weeks ago
- The ExAC browser paper is out in the NAR database issue! Thanks to all contributors esp @BrettThomas + @benweisburd: nar.oxfordjournals.org/content/early/… 2 months ago