NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline
Metagenomic sequencing combined with Oxford Nanopore Technology has the potential to become a point-of-care test for infectious disease in public health and clinical settings, providing rapid diagnosis of infection, guiding individual patient management and treatment strategies, and informing infect...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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Oxford University Press
2020
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| _version_ | 1797085060343529472 |
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| author | Xu, Y Yang-Turner, Y Volk, D Crook, D |
| author_facet | Xu, Y Yang-Turner, Y Volk, D Crook, D |
| author_sort | Xu, Y |
| collection | OXFORD |
| description | Metagenomic sequencing combined with Oxford Nanopore Technology has the potential to become a point-of-care test for infectious disease in public health and clinical settings, providing rapid diagnosis of infection, guiding individual patient management and treatment strategies, and informing infection prevention and control practices. However, publicly available, streamlined, and reproducible pipelines for analyzing Nanopore metagenomic sequencing data are still lacking. Here we introduce NanoSPC, a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data. NanoSPC can identify potentially pathogenic viruses and bacteria simultaneously to provide comprehensive characterization of individual samples. The pipeline can also detect single nucleotide variants and assemble high quality complete consensus genome sequences, permitting high-resolution inference of transmission. We implement NanoSPC using Nextflow manager within Docker images to allow reproducibility and portability of the analysis. 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, Amazon Elastic Computing Cloud, Microsoft Azure and OpenStack. Users could either access our web interface (https://nanospc.mmmoxford.uk) to run cloud-based analysis, monitor process, and visualize results, as well as download Docker images and run command line to analyse data locally. |
| first_indexed | 2024-03-07T02:03:50Z |
| format | Journal article |
| id | oxford-uuid:9e4953d4-171f-4e3a-b41e-13459b219301 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T02:03:50Z |
| publishDate | 2020 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:9e4953d4-171f-4e3a-b41e-13459b2193012022-03-27T00:49:06ZNanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipelineJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:9e4953d4-171f-4e3a-b41e-13459b219301EnglishSymplectic ElementsOxford University Press2020Xu, YYang-Turner, YVolk, DCrook, DMetagenomic sequencing combined with Oxford Nanopore Technology has the potential to become a point-of-care test for infectious disease in public health and clinical settings, providing rapid diagnosis of infection, guiding individual patient management and treatment strategies, and informing infection prevention and control practices. However, publicly available, streamlined, and reproducible pipelines for analyzing Nanopore metagenomic sequencing data are still lacking. Here we introduce NanoSPC, a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data. NanoSPC can identify potentially pathogenic viruses and bacteria simultaneously to provide comprehensive characterization of individual samples. The pipeline can also detect single nucleotide variants and assemble high quality complete consensus genome sequences, permitting high-resolution inference of transmission. We implement NanoSPC using Nextflow manager within Docker images to allow reproducibility and portability of the analysis. 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, Amazon Elastic Computing Cloud, Microsoft Azure and OpenStack. Users could either access our web interface (https://nanospc.mmmoxford.uk) to run cloud-based analysis, monitor process, and visualize results, as well as download Docker images and run command line to analyse data locally. |
| spellingShingle | Xu, Y Yang-Turner, Y Volk, D Crook, D NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline |
| title | NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline |
| title_full | NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline |
| title_fullStr | NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline |
| title_full_unstemmed | NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline |
| title_short | NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline |
| title_sort | nanospc a scalable portable cloud compatible viral nanopore metagenomic data processing pipeline |
| work_keys_str_mv | AT xuy nanospcascalableportablecloudcompatibleviralnanoporemetagenomicdataprocessingpipeline AT yangturnery nanospcascalableportablecloudcompatibleviralnanoporemetagenomicdataprocessingpipeline AT volkd nanospcascalableportablecloudcompatibleviralnanoporemetagenomicdataprocessingpipeline AT crookd nanospcascalableportablecloudcompatibleviralnanoporemetagenomicdataprocessingpipeline |