Windshield splatter analysis with the Galaxy metagenomic pipeline

Pond, S. K., Wadhawan, S., Chiaromonte, F., Ananda, G., Chung, W. Y., Taylor, J., Nekrutenko, A. (October 2009) Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research, 19 (11). pp. 2144-2153.

URL: http://www.ncbi.nlm.nih.gov/pubmed/19819906
DOI: 10.1101/gr.094508.109

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. © 2009 by Cold Spring Harbor Laboratory Press.

Item Type: Paper
Uncontrolled Keywords: phylogenetic profiling sequencing technologies statistical analyses data visualization
Subjects: Investigative techniques and equipment
Investigative techniques and equipment > assays
Investigative techniques and equipment > whole exome sequencing
Investigative techniques and equipment > assays > whole exome sequencing
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Matt Covey
Date: 9 October 2009
Date Deposited: 19 Feb 2013 14:58
Last Modified: 19 Feb 2013 14:58
PMCID: PMC2775585
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27477

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