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).
- Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Cummings BB, Marshall JL, Tukiainen T, Lek M, Donkervoort S, Foley AR, Bolduc V, Waddell LB, Sandaradura SA, O'Grady GL, Estrella E, Reddy HM, Zhao F, Weisburd B, Karczewski KJ, O'Donnell-Luria AH, Birnbaum D, Sarkozy A, Hu Y, Gonorazky H, Claeys K, Joshi H, Bournazos A, Oates EC, Ghaoui R, Davis MR, Laing NG, Topf A, Genotype-Tissue Expression Consortium, Kang PB, Beggs AH, North KN, Straub V, Dowling JJ, Muntoni F, Clarke NF, Cooper ST, Bönnemann CG, MacArthur DG
- Base-Specific Mutational Intolerance Near Splice-Sites Clarifies Role Of Non-Essential Splice Nucleotides @dalygene biorxiv.org/content/early/… 4 days ago
- Front FA: "Welcome to Boston where the local time..." back FA: "Idk where the front of the plane is the back is in philly" 😂😃 @AmericanAir 1 week ago
- RT @skathire: Human genome project gave us ‘parts-list’ of 18,000+ genes. Here, what it means for person to be missing a part 1/ https://t… 1 week ago
- Yay! MAPS was my favorite part of ExAC twitter.com/beryl_bbc/stat… 3 weeks ago
- RT @Eric_Fauman: Useful new phenotype annotation in gnomAD... https://t.co/PlmygavlSj 3 weeks ago