Windshield splatter analysis with the Galaxy metagenomic pipeline

Sergei Kosakovsky Pond, Samir Wadhawan, Francesca Chiaromonte, Guruprasad Ananda, Wen Yu Chung, James Taylor, Anton Nekrutenko

Research output: Contribution to journalArticle

49 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)2144-2153
Number of pages10
JournalGenome research
Volume19
Issue number11
DOIs
StatePublished - Nov 1 2009

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Galaxies
Metagenomics
Statistical Data Interpretation
Workflow
Quality Control
Insects
Publications
Technology
Equipment and Supplies

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Pond, Sergei Kosakovsky ; Wadhawan, Samir ; Chiaromonte, Francesca ; Ananda, Guruprasad ; Chung, Wen Yu ; Taylor, James ; Nekrutenko, Anton. / Windshield splatter analysis with the Galaxy metagenomic pipeline. In: Genome research. 2009 ; Vol. 19, No. 11. pp. 2144-2153.
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Windshield splatter analysis with the Galaxy metagenomic pipeline. / Pond, Sergei Kosakovsky; Wadhawan, Samir; Chiaromonte, Francesca; Ananda, Guruprasad; Chung, Wen Yu; Taylor, James; Nekrutenko, Anton.

In: Genome research, Vol. 19, No. 11, 01.11.2009, p. 2144-2153.

Research output: Contribution to journalArticle

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Pond SK, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J et al. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome research. 2009 Nov 1;19(11):2144-2153. https://doi.org/10.1101/gr.094508.109