This is especially the case when a more complex approach that combines multiple tools is required to generate meaningful results for a given study. BWA and GATK).ĭespite the large number of tools, the bottleneck in a typical sequencing project remains in the bioinformatics analysis phase due to lack of access to informatics expertise. Many of these tools are constantly being improved and updated, with new versions released on a frequent basis (e.g. CONTRA, ExomeCNV and TREAT), while others are also applicable to sequence data generated by other technologies. Some of these methods are specifically tailored to TR data (e.g. These methods include: FastQC ( ) and htSeqTools for assessing the quality of short-read data BWA and Bowtie2 for sequence alignment MuTect and GATK for detecting single-nucleotide variations CONTRA and ExomeCNV for identifying copy number aberrations Genome MuSiC and MutSig ( ) for conducting pathway analysis and, TREAT and VarSifter for annotation and visualization. Coupled with the popularity of TR is the deluge of bioinformatics tools that have been developed to analyse sequence data, with over 570 tools published within a span of only 2 years. Moreover, with reducing costs of sequencing, TR technologies are becoming an increasingly attractive and feasible option for smaller research groups and clinical laboratories to undertake sequencing projects. the 1000 genomes project ) and on human diseases – have benefited greatly from this sequencing technology. Previous studies on genetic diversity (e.g. Targeted resequencing (TR) by massively parallel sequencing, which includes whole-exome sequencing (WES), is a well-established and cost-effective means to analyse specific regions of a genome. This does not alter our adherence to PLOS ONE policies on sharing data and materials. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: YourGene Biosciences Australia has provided support on cloud technology, Virtual Machine development, and drafting of manuscript (through author Isaam Saeed). Papenfuss was supported by an NHMRC Career Development Fellowship. This work was supported by the Victorian Breast Cancer Research Consortium and Australian Research Council (grant DP1096296), and was also supported by grants and a fellowship of the NHMRC and the VCA to G.A. This work was also supported by Program Grant 633004 of the National Health and Medical Research Council of Australia (NHMRC) and Translational Research Program Grant 10/TPG/1-02 of the Cancer Institute New South Wales. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.įunding: This project was enabled by the Melbourne Melanoma Project funded by the Victorian Government through the Victorian Cancer Agency (VCA) Translational Research Program Grant (EOI09_27). Received: JanuAccepted: MaPublished: April 21, 2014Ĭopyright: © 2014 Li et al. (2014) Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment. Ĭitation: Li J, Doyle MA, Saeed I, Wong SQ, Mar V, Goode DL, et al. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. 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. 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. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. 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. 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.
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