Windshield splatter analysis with the Galaxy metagenomic pipeline

• Type of Material: Article
• Authors: Sergei Kosakovsky Pond, School of Medicine University of California San Diego; Samir Wadhawan, Penn State University; Francesca Chiaromonte, Penn State University; Guruprasad Ananda, Penn State University; Wen-Yu Chung, Penn State University; James Taylor, Emory University; Anton Nekrutenko, Penn State University
• Language: English
• Date: 2009-11
• Publisher: Cold Spring Harbor Laboratory Press
• Publication Version: Final Published Version
• Copyright Statement: © 2009 by Cold Spring Harbor Laboratory Press/Freely available online through the Genome Research Open Access option.
• Final Published Version (URL): http://genome.cshlp.org/content/19/11/2144
• Title of Journal or Parent Work: Genome Research
• ISSN: 1088-9051
• Volume: 19
• Issue: 11
• Start Page: 2144
• End Page: 2153
• Grant/Funding Information: NSF grant DMS-071499 to S.K.P.; Funded by Beckman Foundation Young Investigator Award to A.N.; A grant with the Pennsylvania Department of Health using Tobacco Settlement Funds; Funds from Penn State University and the Huck Institutes for the Life Sciences to A.N.; Emory University to J.T.; NSF grant DBI 0543285; NIH grant HG004909 to A.N. and J.T.
• Research Categories: Health Sciences, General; Biology, General

Abstract

How many species inhabit our immediate surroundings? A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds. The windshield of a moving vehicle is subjected to numerous insect strikes and can be used as a collection device for representative sampling. Unfortunately the analysis of biological material collected in that manner, as with most metagenomic studies, proves to be rather demanding due to the large number of required tools and considerable computational infrastructure. In this study, we use organic matter collected by a moving vehicle to design and test a comprehensive pipeline for phylogenetic profiling of metagenomic samples that includes all steps from processing and quality control of data generated by next-generation sequencing technologies to statistical analyses and data visualization. To the best of our knowledge, this is also the first publication that features a live online supplement providing access to exact analyses and workflows used in the article.