STORMSeq: An open-source, user-friendly pipeline for processing personal genomics data in the cloud

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Karczewski, Konrad J ^a   Fernald, Guy Haskin ^a   Martin, Alicia R ^a   Snyder, Michael ^a   Tatonetti, Nicholas P ^b   Dudley, Joel T ^c  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

^c MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA BASE; EXOME; GENE SEQUENCE; GENOMICS; HUMAN; HUMAN GENETICS; STORMSEQ DATABASE; HUMAN GENOME;

GENOME, HUMAN; HUMANS; USER-COMPUTER INTERFACE;

EID: 84898639657     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0084860     Document Type: Article

References (12)

1. Goecks J, Nekrutenko A, Taylor J, Galaxy Team (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11:R86. doi:10.1186/gb-2010-11-8-r86.
2. Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL (2009) Searching for SNPs with cloud computing. Genome Biol 10:R134. doi:10.1186/gb-2009-10-11-r134.
3. Fischer M, Snajder R, Pabinger S, Dander A, Schossig A, et al. (2012) SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data. PLoS ONE 7:e41948. doi:10.1371/journal.pone.0041948.
4. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760. doi:10.1093/ bioinformatics/btp324.
5. Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv.
6. Faster and More Accurate Sequence Alignment with SNAP (2011) Faster and More Accurate Sequence Alignment with SNAP. arXiv.
7. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491-498. doi:10.1038/ng.806.
8. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079. doi:10.1093/bioinformatics/btp352.
9. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, et al. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26:2069-2070. doi:10.1093/bioinformatics/btq330.
10. Yin T, Cook D, Lawrence M (2012) ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biology 13:R77. doi:10.1186/gb-2012-13-8-r77.
11. Bostock M, Ogievetsky V, Heer J (2011) D Data-Driven Documents. Visualization and Computer Graphics, IEEE Transactions on 17:2301-2309. doi:10.1109/TVCG.2011.185.
12. Karczewski KJ, Tirrell RP, Cordero P, Tatonetti NP, Dudley JT, et al. (2012) Interpretome: a freely available, modular, and secure personal genome interpretation engine. Pac Symp Biocomput: 339-350.