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 language | English (US) |
|---|---|
| Pages (from-to) | 2144-2153 |
| Number of pages | 10 |
| Journal | Genome research |
| Volume | 19 |
| Issue number | 11 |
| DOIs | |
| State | Published - Nov 1 2009 |
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All Science Journal Classification (ASJC) codes
- Genetics
- Genetics(clinical)
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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 journal › Article
TY - JOUR
T1 - Windshield splatter analysis with the Galaxy metagenomic pipeline
AU - Pond, Sergei Kosakovsky
AU - Wadhawan, Samir
AU - Chiaromonte, Francesca
AU - Ananda, Guruprasad
AU - Chung, Wen Yu
AU - Taylor, James
AU - Nekrutenko, Anton
PY - 2009/11/1
Y1 - 2009/11/1
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=70350731109&partnerID=8YFLogxK
U2 - 10.1101/gr.094508.109
DO - 10.1101/gr.094508.109
M3 - Article
C2 - 19819906
AN - SCOPUS:70350731109
VL - 19
SP - 2144
EP - 2153
JO - Genome Research
JF - Genome Research
SN - 1088-9051
IS - 11
ER -