Windshield splatter analysis with the Galaxy metagenomic pipeline

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

doi:10.1101/gr.094508.109

Cited by 70 publications

(37 citation statements)

References 42 publications

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“…Profiling of the microbiome was performed using the metagenomic tools available in the Galaxy Public Server [47] following the metagenomic pipeline described by Kasakovsky Pond et al [48]. Briefly, sequences were filtered to exclude reads with a quality score <20 and a contiguous length <250 bp.…”

Section: Methodsmentioning

confidence: 99%

The murine appendiceal microbiome is altered in spontaneous colitis and its pathological progression

et al. 2014

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BackgroundInflammatory bowel disease (comprising ulcerative colitis and Crohn’s disease) is a multifactorial disease that is extensively associated with stool microbiome changes (dysbiosis). Appendicitis and appendectomy limits subsequent colitis, clinically, and in animal models. We wanted to examine how the appendiceal and stool microbiome fared in our spontaneous colitic Winnie (Muc2−/−) mice model.MethodsTwo C57BL/6 and 10 Winnie mice at ages 12 and 15 weeks were euthanized for stool and caecal patch samples. DNA was extracted using the QIAamp DNA Stool Mini Kit then the V1-V3 hypervariable region of the 16S rRNA gene was sequenced using the Roche/454 GS FLX + pyrosequencing instrument. A Galaxy metagenomic pipeline was used to define phyla and families at sequence similarity threshold of ≥ 80%.ResultsBacteriodetes was decreased in 15-week Winnie mice appendices compared to corresponding stool samples (P < 0.01). Proteobacteria was increased in appendices of Winnie mice compared to corresponding stool samples (P < 0.05). The Bacteroidetes family Rikenellaceae could be identified only in 15-week-old Winnie mice appendices. A higher quantity of Acetobacteraceae (Proteobacteria phylum) was present in 15-week Winnie mice when compared to 12-week Winnie mice (P < 0.01). Helicobacteraceae (Proteobacteria phylum), which is prominent in all Winnie mice, is absent in control mice.ConclusionsThe appendiceal dysbiosis observed in our Winnie mice is commensurate with, and adds to extant literature data. The presence of Helicobacteraceae (Proteobacteria) only in colitic Winnie mice (but not control mice) is consistent with reports of increased Helicobacter in IBD patients. Bacteroides (Bacteroidetes) decreases may be a reflection of reduced anti-inflammatory commensal species such as B. fragilis. Further research is warranted to expand and delineate the relationship between IBD and the appendix microbiome.

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Section: Methodsmentioning

confidence: 99%

The murine appendiceal microbiome is altered in spontaneous colitis and its pathological progression

et al. 2014

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“…Figure 9 (left) shows a flow chart representation of a metagenomics workflow deposited on the Galaxy public pages [46,47]. The input to this workflow is a set of NGS reads and associated quality data.…”

Section: Resultsmentioning

confidence: 99%

“…In the original implementation of this workflow on Galaxy [46,47], and as depicted in the schematic representation of Figure 9, we can identify two issues: First, the input reads are passed to MegaBLAST is a single multi-FASTA file which implies sequential processing of the queries against the database. Second, there are two nodes for MegaBLAST: one to consider the NCBI_WGS database and the other to consider the NCBI_NT database.…”

Section: Resultsmentioning

confidence: 99%

Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support

2012

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BackgroundOver the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts.ResultsIn this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure.ConclusionsTavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub-) workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis.The system can be accessed either through a cloud-enabled web-interface or downloaded and installed to run within the user's local environment. All resources related to Tavaxy are available at http://www.tavaxy.org.

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“…We used the windshield dataset of [31], which is composed of two collections of 454 FLX reads. These reads came from the DNA of the organic matter on the windshield of a moving vehicle that visited two geographic locations (trips A and B).…”

Section: Resultsmentioning

confidence: 99%

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package

et al. 2012

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BackgroundBioinformatics services have been traditionally provided in the form of a web-server that is hosted at institutional infrastructure and serves multiple users. This model, however, is not flexible enough to cope with the increasing number of users, increasing data size, and new requirements in terms of speed and availability of service. The advent of cloud computing suggests a new service model that provides an efficient solution to these problems, based on the concepts of "resources-on-demand" and "pay-as-you-go". However, cloud computing has not yet been introduced within bioinformatics servers due to the lack of usage scenarios and software layers that address the requirements of the bioinformatics domain.ResultsIn this paper, we provide different use case scenarios for providing cloud computing based services, considering both the technical and financial aspects of the cloud computing service model. These scenarios are for individual users seeking computational power as well as bioinformatics service providers aiming at provision of personalized bioinformatics services to their users. We also present elasticHPC, a software package and a library that facilitates the use of high performance cloud computing resources in general and the implementation of the suggested bioinformatics scenarios in particular. Concrete examples that demonstrate the suggested use case scenarios with whole bioinformatics servers and major sequence analysis tools like BLAST are presented. Experimental results with large datasets are also included to show the advantages of the cloud model.ConclusionsOur use case scenarios and the elasticHPC package are steps towards the provision of cloud based bioinformatics services, which would help in overcoming the data challenge of recent biological research. All resources related to elasticHPC and its web-interface are available at http://www.elasticHPC.org.

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Windshield splatter analysis with the Galaxy metagenomic pipeline

Cited by 70 publications

References 42 publications

The murine appendiceal microbiome is altered in spontaneous colitis and its pathological progression

The murine appendiceal microbiome is altered in spontaneous colitis and its pathological progression

Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package

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