Windshield splatter analysis with the Galaxy metagenomic pipeline

Sergei Kosakovsky Pond; Samir Wadhawan; Francesca Chiaromonte; Guruprasad Ananda; Wen-Yu Chung; James Taylor; Anton Nekrutenko; The Galaxy Team

doi:10.1101/gr.094508.109

Windshield splatter analysis with the Galaxy metagenomic pipeline

¹ http://galaxyproject.org;
² Division of Infectious Diseases, Division of Biomedical Informatics, School of Medicine University of California San Diego, San Diego, California 92103, USA;
³ Huck Institute for the Life Sciences, Penn State University, University Park, Pennsylvania 16803, USA;
⁴ Department of Statistics, Penn State University, University Park, Pennsylvania 16803, USA;
⁵ Departments of Biology and Mathematics & Computer Science, Emory University, Atlanta, Georgia 30322, USA

↵7 Present addresses: Department of Genetics, University of Pennsylvania Medical School, 415 Curie Blvd., Philadelphia, PA 19104, USA;
↵8 Cold Spring Harbor Laboratory, One Bungtown Rd., Cold Spring Harbor, NY 11724, USA.

↵6 These authors contributed equally to this work.

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.

Footnotes

↵9 Corresponding authors.

E-mail spond{at}ucsd.edu; fax (619) 543-5094.

E-mail james.taylor{at}emory.edu; fax (404) 727-2880.

E-mail anton{at}bx.psu.edu; fax (814) 863-6699.
[Supplemental material is available online at http://www.genome.org. All data and tools described in this manuscript can be downloaded or used directly at http://galaxyproject.org. Exact analyses and workflows used in this paper are available at http://usegalaxy.org/u/aun1/p/windshield-splatter.]
Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.094508.109.
- Received March 31, 2009.
- Accepted August 19, 2009.