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ASA(3)P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates
Whole genome sequencing of bacteria has become daily routine in many fields. Advances in DNA sequencing technologies and continuously dropping costs have resulted in a tremendous increase in the amounts of available sequence data. However, comprehensive in-depth analysis of the resulting data remain...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7077848/ https://www.ncbi.nlm.nih.gov/pubmed/32134915 http://dx.doi.org/10.1371/journal.pcbi.1007134 |
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author | Schwengers, Oliver Hoek, Andreas Fritzenwanker, Moritz Falgenhauer, Linda Hain, Torsten Chakraborty, Trinad Goesmann, Alexander |
author_facet | Schwengers, Oliver Hoek, Andreas Fritzenwanker, Moritz Falgenhauer, Linda Hain, Torsten Chakraborty, Trinad Goesmann, Alexander |
author_sort | Schwengers, Oliver |
collection | PubMed |
description | Whole genome sequencing of bacteria has become daily routine in many fields. Advances in DNA sequencing technologies and continuously dropping costs have resulted in a tremendous increase in the amounts of available sequence data. However, comprehensive in-depth analysis of the resulting data remains an arduous and time-consuming task. In order to keep pace with these promising but challenging developments and to transform raw data into valuable information, standardized analyses and scalable software tools are needed. Here, we introduce ASA(3)P, a fully automatic, locally executable and scalable assembly, annotation and analysis pipeline for bacterial genomes. The pipeline automatically executes necessary data processing steps, i.e. quality clipping and assembly of raw sequencing reads, scaffolding of contigs and annotation of the resulting genome sequences. Furthermore, ASA(3)P conducts comprehensive genome characterizations and analyses, e.g. taxonomic classification, detection of antibiotic resistance genes and identification of virulence factors. All results are presented via an HTML5 user interface providing aggregated information, interactive visualizations and access to intermediate results in standard bioinformatics file formats. We distribute ASA(3)P in two versions: a locally executable Docker container for small-to-medium-scale projects and an OpenStack based cloud computing version able to automatically create and manage self-scaling compute clusters. Thus, automatic and standardized analysis of hundreds of bacterial genomes becomes feasible within hours. The software and further information is available at: asap.computational.bio. |
format | Online Article Text |
id | pubmed-7077848 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-70778482020-03-23 ASA(3)P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates Schwengers, Oliver Hoek, Andreas Fritzenwanker, Moritz Falgenhauer, Linda Hain, Torsten Chakraborty, Trinad Goesmann, Alexander PLoS Comput Biol Research Article Whole genome sequencing of bacteria has become daily routine in many fields. Advances in DNA sequencing technologies and continuously dropping costs have resulted in a tremendous increase in the amounts of available sequence data. However, comprehensive in-depth analysis of the resulting data remains an arduous and time-consuming task. In order to keep pace with these promising but challenging developments and to transform raw data into valuable information, standardized analyses and scalable software tools are needed. Here, we introduce ASA(3)P, a fully automatic, locally executable and scalable assembly, annotation and analysis pipeline for bacterial genomes. The pipeline automatically executes necessary data processing steps, i.e. quality clipping and assembly of raw sequencing reads, scaffolding of contigs and annotation of the resulting genome sequences. Furthermore, ASA(3)P conducts comprehensive genome characterizations and analyses, e.g. taxonomic classification, detection of antibiotic resistance genes and identification of virulence factors. All results are presented via an HTML5 user interface providing aggregated information, interactive visualizations and access to intermediate results in standard bioinformatics file formats. We distribute ASA(3)P in two versions: a locally executable Docker container for small-to-medium-scale projects and an OpenStack based cloud computing version able to automatically create and manage self-scaling compute clusters. Thus, automatic and standardized analysis of hundreds of bacterial genomes becomes feasible within hours. The software and further information is available at: asap.computational.bio. Public Library of Science 2020-03-05 /pmc/articles/PMC7077848/ /pubmed/32134915 http://dx.doi.org/10.1371/journal.pcbi.1007134 Text en © 2020 Schwengers et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Schwengers, Oliver Hoek, Andreas Fritzenwanker, Moritz Falgenhauer, Linda Hain, Torsten Chakraborty, Trinad Goesmann, Alexander ASA(3)P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates |
title | ASA(3)P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates |
title_full | ASA(3)P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates |
title_fullStr | ASA(3)P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates |
title_full_unstemmed | ASA(3)P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates |
title_short | ASA(3)P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates |
title_sort | asa(3)p: an automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7077848/ https://www.ncbi.nlm.nih.gov/pubmed/32134915 http://dx.doi.org/10.1371/journal.pcbi.1007134 |
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