TY - JOUR
T1 - Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes
T2 - A virtual appliance approach for instant deployment
AU - Li, Jason
AU - Doyle, Maria A.
AU - Saeed, Isaam
AU - Wong, Stephen Q.
AU - Mar, Victoria
AU - Goode, David L.
AU - Caramia, Franco
AU - Doig, Ken
AU - Ryland, Georgina L.
AU - Thompson, Ella R.
AU - Hunter, Sally M.
AU - Halgamuge, Saman K.
AU - Ellul, Jason
AU - Dobrovic, Alexander
AU - Campbell, Ian G.
AU - Papenfuss, Anthony T.
AU - McArthur, Grant A.
AU - Tothill, Richard W.
PY - 2014/4/21
Y1 - 2014/4/21
N2 - Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics. petermac.org/treva/.
AB - Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics. petermac.org/treva/.
UR - http://www.scopus.com/inward/record.url?scp=84899697726&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0095217
DO - 10.1371/journal.pone.0095217
M3 - Article
C2 - 24752294
AN - SCOPUS:84899697726
SN - 1932-6203
VL - 9
SP - e95217
JO - PLoS ONE
JF - PLoS ONE
IS - 4
M1 - e95217
ER -