SeqBench: Integrated solution for the management and analysis of exome sequencing data

BMC Research Notes

Volumn 7, Issue 1, 2014, Pages

  Dander, Andreas ^a,b   Pabinger, Stephan ^a,c   Sperk, Michael ^a,d   Fischer, Maria ^a   Stocker, Gernot ^a   Trajanoski, Zlatko ^a,b  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

^b Oncotyrol Center for Personalized Cancer Medicine   (Austria)

^c AIT AUSTRIAN INSTITUTE OF TECHNOLOGY   (Austria)

^d ADSI   (Austria)

Author keywords

Cloud; Data analysis; Exome; Open source; Sequencing; Virtual machine image; Web application

Indexed keywords

ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; EQUIPMENT; EXOME; HIGH THROUGHPUT SEQUENCING; METHODOLOGY;

EXOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84892473851     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-7-43     Document Type: Article

References (11)

1. Mutations in ROGDI Cause Kohlschütter-Tönz Syndrome. Schossig A, Wolf NI, Fischer C, Fischer M, Stocker G, Pabinger S, Dander A, Steiner B, Tönz O, Kotzot D, Haberlandt E, Amberger A, Burwinkel B, Wimmer K, Fauth C, Grond-Ginsbach C, Koch MJ, Deichmann A, von Kalle C, Bartram CR, Kohlschütter A, Trajanoski Z, Zschocke J, Am J Hum Genet 2012 90 4 701 707 [PMID: 22424600] 10.1016/j.ajhg.2012.02.012 22424600
2. Mutations of DEPDC5 cause autosomal dominant focal epilepsies. Ishida S, Picard F, Rudolf G, Noé E, Achaz G, Thomas P, Genton P, Mundwiller E, Wolff M, Marescaux C, Miles R, Baulac M, Hirsch E, Leguern E, Baulac S, Nat Genet 2013 45 552 555 [PMID: 23542701] 10.1038/ng.2601 23542701
3. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Dulak AM, Stojanov P, Peng S, Lawrence MS, Fox C, Stewart C, Bandla S, Imamura Y, Schumacher SE, Shefler E, McKenna A, Carter SL, Cibulskis K, Sivachenko A, Saksena G, Voet D, Ramos AH, Auclair D, Thompson K, Sougnez C, Onofrio RC, Guiducci C, Beroukhim R, Zhou Z, Lin L, Lin J, Reddy R, Chang A, Landrenau R, Pennathur A, et al. Nat Genet 2013 45 478 486 [PMID: 23525077] 10.1038/ng.2591 23525077
4. A survey of tools for variant analysis of next-generation genome sequencing data. Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z, Brief Bioinform 2013 [PMID: 23341494]
5. SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data. Fischer M, Snajder R, Pabinger S, Dander A, Schossig A, Zschocke J, Trajanoski Z, Stocker G, PloS One 2012 7 8 41948 [PMID: 22870267] 10.1371/journal.pone.0041948 22870267
6. NG6: Integrated next generation sequencing storage and processing environment. Mariette J, Escudié F, Allias N, Salin G, Noirot C, Thomas S, Klopp C, BMC Genomics 2012 13 462 [PMID: 22958229] 10.1186/1471-2164-13-462 22958229
7. Galaxy LIMS for next-generation sequencing. Scholtalbers J, Rößler J, Sorn P, Graaf Jd, Boisguérin V, Castle J, Sahin U, Bioinformatics 2013 29 9 1233 1234 [PMID: 23479349] 10.1093/bioinformatics/ btt115 23479349
8. Next generation tools for genomic data generation, distribution, and visualization. Nix DA, Di Sera TL, Dalley BK, Milash BA, Cundick RM, Quinn KS, Courdy SJ, BMC Bioinformatics 2010 11 455 [PMID: 20828407] 10.1186/1471-2105-11- 455 20828407
9. openBIS: a flexible framework for managing and analyzing complex data in biology research. Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmström L, Aebersold R, Rinn B, BMC Bioinformatics 2011 12 468 [PMID: 22151573] 10.1186/1471-2105-12-468 22151573
10. MEMOSys: Bioinformatics platform for genome-scale metabolic models. Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z, BMC Syst Biol 2011 5 20 [PMID: 21276275] 10.1186/1752-0509-5-20 21276275
11. Harnessing virtual machines to simplify next generation DNA sequencing analysis. Nocq J, Celton M, Gendron P, Lemieux S, Wilhelm BT, Bioinformatics 2013 29 17 2075 2083 [PMID: 23786767] 10.1093/bioinformatics/btt352 23786767