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Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach

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dc.contributor.author Dickins, Benjamin
dc.contributor.author Rebolledo-Jaramillo, Boris
dc.contributor.author Su, Marcia Shu-Wei
dc.contributor.author Paul, Ian M.
dc.contributor.author Blankenberg, Daniel
dc.contributor.author Stoler, Nicholas
dc.contributor.author Makova, Kateryna D.
dc.contributor.author Nekrutenko, Anton
dc.date.accessioned 2019-07-11T00:20:27Z
dc.date.available 2019-07-11T00:20:27Z
dc.date.issued 2014
dc.identifier.citation Biotechniques, 2014, Vol. 56, n° 3, pp. 134-+
dc.identifier.uri http://hdl.handle.net/11447/2523
dc.identifier.uri http://dx.doi.org/10.2144/000114146
dc.description.abstract Polymorphism discovery is a routine application of next-generation sequencing technology where multiple samples are sent to a service provider for library preparation, subsequent sequencing, and bioinformatic analyses. The decreasing cost and advances in multiplexing approaches have made it possible to analyze hundreds of samples at a reasonable cost. However, because of the manual steps involved in the initial processing of samples and handling of sequencing equipment, cross-contamination remains a significant challenge. It is especially problematic in cases where polymorphism frequencies do not adhere to diploid expectation, for example, heterogeneous tumor samples, organellar genomes, as well as during bacterial and viral sequencing. In these instances, low levels of contamination may be readily mistaken for polymorphisms, leading to false results. Here we describe practical steps designed to reliably detect contamination and uncover its origin, and also provide new, Galaxy-based, readily accessible computational tools and workflows for quality control. All results described in this report can be reproduced interactively on the web as described at http://usegalaxy.org/contamination.
dc.language.iso en
dc.subject Re-sequencing
dc.subject Contamination
dc.subject Next-generation sequencing
dc.subject Galaxy
dc.subject Reproducibility
dc.title Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach
dc.type Article


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