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A scalable data analysis platform for metagenomics
2013
2013 IEEE International Conference on Big Data
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Shock and AWE can be used to build a scalable and reproducible data analysis infrastructure for upper-level biological data analysis services. ...
To address the computational challenges posed by this workload, we developed a new data analysis platform, including a data management system (Shock) for biological sequence data and a workflow management ...
As a product, we have developed the Shock data management and AWE workflow management system which can be used to build a scalable a data analysis platform. ...
doi:10.1109/bigdata.2013.6691723
dblp:conf/bigdataconf/TangWDGWM13
fatcat:n5w2eavmtraehhzkx35tydliai
NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline
2020
Nucleic Acids Research
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Here we introduce NanoSPC, a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data. ...
Moreover, we deploy NanoSPC to our scalable pathogen pipeline platform, enabling elastic computing for high throughput Nanopore data on HPC cluster as well as multiple cloud platforms, such as Google Cloud ...
CONCLUSION We report NanoSPC, a scalable, portable, and cloud compatibilable pipeline for analyzing metagenomic sequencing data generated using ONT. ...
doi:10.1093/nar/gkaa413
pmid:32442274
fatcat:6dtk4z4yqjdtjnocm3xnjozsia
META-pipe - Pipeline Annotation, Analysis and Visualization of Marine Metagenomic Sequence Data
[article]
2016
arXiv
pre-print
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We provide a new pipeline, META-pipe, for marine metagenomics analysis. It offers pre- processing, assembly, taxonomic classification and functional analysis. ...
We have evaluated the scalability and performance of the analysis pipeline. ...
There is therefore a need to develop a scalable pipeline for the marine metagenomics field. ...
arXiv:1604.04103v1
fatcat:i5qw7db6jfgohpbtq3t4oymmca
Web Resources for Metagenomics Studies
2015
Genomics, Proteomics & Bioinformatics
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The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. ...
In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. ...
Acknowledgments The authors are thankful to BIT Virtual Centre, Patan Node, Hemchandracharya North Gujarat University, India for providing servers and computational facilities. ...
doi:10.1016/j.gpb.2015.10.003
pmid:26602607
pmcid:PMC4678780
fatcat:uldztj42fbdqvbq55u3poyigeq
Workload characterization for MG-RAST metagenomic data analytics service in the cloud
2014
2014 IEEE International Conference on Big Data (Big Data)
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For example, MG-RAST, a production open-public metagenome annotation service, has experienced increasingly large amount of data submission and has demanded scalable resources for the computational needs ...
The consequent data deluge has imposed big burdens for data analysis applications. ...
ACKNOWLEDGMENTS This work was supported in part by the NIH award U01HG006537 "OSDF: Support infrastructure for NextGen sequence storage, analysis, and management", and U.S. ...
doi:10.1109/bigdata.2014.7004394
dblp:conf/bigdataconf/TangBDMGHWM14
fatcat:4qcliocqhbfyxam2ch26dmst2u
A Review of Scalable Bioinformatics Pipelines
2017
Data Science and Engineering
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Scalability is increasingly important for bioinformatics analysis services, since these must handle larger datasets, more jobs, and more users. ...
We also discuss current trends for bioinformatics pipeline development. ...
GESALL Variant Calling Pipeline GESALL [21] is a genomic analysis platform for unmodified analysis tools that use the POSIX file system interface. ...
doi:10.1007/s41019-017-0047-z
fatcat:7wyzccy7ffhjdd46pfmljrzioy
Flexible metagenome analysis using the MGX framework
2018
Microbiome
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Conclusions: With MGX, we provide a novel metagenome analysis platform giving researchers access to the most recent analysis tools. ...
Results: We present MGX, a flexible and extensible client/server-framework for the management and analysis of metagenomic datasets; MGX features a comprehensive set of adaptable workflows required for ...
Acknowledgements Funding for the operation and maintenance of MGX is provided by the German Federal Ministry of Education and Research (BMBF) project "Bielefeld-Gießen Center for Microbial Bioinformatics-BiGi ...
doi:10.1186/s40168-018-0460-1
pmid:29690922
pmcid:PMC5937802
fatcat:a5sd3o6lpbbcjdioaoo6jar2zq
Metagenome2Vec: Building Contextualized Representations for Scalable Metagenome Analysis
[article]
2021
arXiv
pre-print
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Given the high volume of metagenome sequences, there is a need for scalable frameworks to analyze and segment metagenome sequences from clinical samples, which can be highly imbalanced. ...
There is an increased need for learning robust representations from metagenome reads since pathogens within a family can have highly similar genome structures (some more than 90%) and hence enable the ...
Andres Espindola (Institute of Biosecurity and Microbial Forensics, Oklahoma State University) for providing access and assisting with use of the MiFi platform. ...
arXiv:2111.08001v1
fatcat:4cj5uwdumveynpyivhnt53gi3q
METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics
2010
Computer applications in the biosciences : CABIOS
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A data management layer allows collaborative data analysis and result sharing. Availability: Website ...
JCVI Metagenomics Reports (METAREP) is a Web 2.0 application designed to help scientists analyze and compare annotated metagenomics data sets. ...
WEB ANALYSIS FEATURES The METAREP View pages provide high level summaries for a dataset (Fig 1 A) . Each tab provides a ranked list and bar chart for the respective data type. ...
doi:10.1093/bioinformatics/btq455
pmid:20798169
pmcid:PMC2951084
fatcat:yrcth3x7rbeuzdifk6tmdicyzm
SparkBLAST: scalable BLAST processing using in-memory operations
2017
BMC Bioinformatics
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The demand for processing ever increasing amounts of genomic data has raised new challenges for the implementation of highly scalable and efficient computational systems. ...
As a proof of concept, some radionuclide-resistant bacterial genomes were selected for similarity analysis. ...
Acknowledgements The authors would like to thank Thais Martins for help with input data preparation, and Rodrigo Jardim for data preparation and preliminary RBH analysis. ...
doi:10.1186/s12859-017-1723-8
pmid:28655296
pmcid:PMC5488373
fatcat:gn5gxf5oxvdgdiri6xhquoe4my
Analysis of Metagenomics Data
[chapter]
2011
Bioinformatics for High Throughput Sequencing
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This service has removed one of the primary bottlenecks in metagenome sequence analysis, the availability of high-performance computing for annotating data. ...
In MG-RAST, all users retain full control of their data, and everything is available for download in a variety of formats. ...
The MG-RAST server is the most widely used tool for the analysis of shotgun metagenomics and provides a basis for sequence analysis of large, complex data sets. ...
doi:10.1007/978-1-4614-0782-9_13
fatcat:62me5g4mbre2pjgpeh3zko5aa4
BugSeq: a highly accurate cloud platform for long-read metagenomic analyses
[article]
2020
bioRxiv
pre-print
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As the use of nanopore sequencing for metagenomic analysis increases, tools capable of performing long-read taxonomic classification in a fast and accurate manner are needed. ...
Results: We present BugSeq, a novel, highly accurate metagenomic classifier for nanopore reads. ...
Resulting data, including quality control and metagenomic classification, was packaged into two HTML files (Supplementary Material), and showed superior accuracy compared with the original WIMP analysis ...
doi:10.1101/2020.10.08.329920
fatcat:vs3tkdimwrfgrdunb5t2mkrale
MetaGeniE: Characterizing Human Clinical Samples Using Deep Metagenomic Sequencing
2014
PLoS ONE
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Among the primary challenges of clinical metagenomic sequencing is the rapid filtering of human reads to survey for pathogens with high specificity and sensitivity. ...
This variation in metagenomes typically manifests in sequencing datasets as low pathogen abundance, a high number of host reads, and the presence of close relatives and complex microbial communities. ...
Analyzed the data: AR. Contributed reagents/ materials/analysis tools: EMD PK JTF AR. Wrote the paper: AR DME JTF. ...
doi:10.1371/journal.pone.0110915
pmid:25365329
pmcid:PMC4218713
fatcat:n76wfhkklrfnpcyj6fvoal73ze
SpaRC: Scalable Sequence Clustering using Apache Spark
[article]
2018
bioRxiv
pre-print
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with rapid development/deployment cycles for similar large scale sequence data analysis problems. ...
It achieved a near linear scalability with respect to input data size and number of compute nodes. ...
For data scalability test we use 20GB, 40GB, 60GB, 80GB, 249 and 100GB fastq datasets from Cow Rumen metagenome. ...
doi:10.1101/246496
fatcat:3qdr2rvcmzcbxiqrjjlm3lh5ry
Towards Solving The Metagenomics Reproducibility Crisis With Cwl And Ro
2018
Zenodo
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Both metagenome data and computation with metagenomes are expensive [Thomas], significant degrees of freedom exists for the computational analysis underscoring the need for reproducibility in the field ...
The MG-RAST portal [Meyer] and its European sister project MGnify [Mitchell] at the European Bioinformatics Institute (EMBL-EBI) provide metagenome analysis services to a large, international community ...
Microbiome puzzle challenge
Distributed containerized workflows
Skyport --a scalable platform for distributed data centric
reproducible computing
• Multiple backends ("cloud", bare-metal, legacy ...
doi:10.5281/zenodo.1484480
fatcat:zillrhyup5hsbc7vobrjmlz3ai
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