Windshield splatter analysis with the Galaxy metagenomic pipeline.
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.
Kosakovsky Pond
Sergei
S
http://galaxyproject.org. spond@ucsd.edu
Wadhawan
Samir
S
Chiaromonte
Francesca
F
Ananda
Guruprasad
G
Chung
Wen-Yu
WY
Taylor
James
J
Nekrutenko
Anton
A
D000465:Algorithms; D000818:Animals; D001336:Automobiles; D001419:Bacteria / Q000145:classification / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification*; D004269:DNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification; D030561:Databases, Nucleic Acid; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D010802:Phylogeny; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
D004269:DNA, Bacterial; D004247:DNA