MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data

The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through re...

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Autores principales: Caboche, Ségolène, Even, Gaël, Loywick, Alexandre, Audebert, Christophe, Hot, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738152/
https://www.ncbi.nlm.nih.gov/pubmed/29258574
http://dx.doi.org/10.1186/s13059-017-1367-z
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author Caboche, Ségolène
Even, Gaël
Loywick, Alexandre
Audebert, Christophe
Hot, David
author_facet Caboche, Ségolène
Even, Gaël
Loywick, Alexandre
Audebert, Christophe
Hot, David
author_sort Caboche, Ségolène
collection PubMed
description The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis. MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of antibiotic susceptibility and resistance and comparing the results of several samples. MICRA is fast, producing few false-positive annotations and variant calls compared to current methods, making it a tool of great interest for fully exploiting sequencing data. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1367-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-57381522017-12-21 MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data Caboche, Ségolène Even, Gaël Loywick, Alexandre Audebert, Christophe Hot, David Genome Biol Software The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis. MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of antibiotic susceptibility and resistance and comparing the results of several samples. MICRA is fast, producing few false-positive annotations and variant calls compared to current methods, making it a tool of great interest for fully exploiting sequencing data. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1367-z) contains supplementary material, which is available to authorized users. BioMed Central 2017-12-19 /pmc/articles/PMC5738152/ /pubmed/29258574 http://dx.doi.org/10.1186/s13059-017-1367-z Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Caboche, Ségolène
Even, Gaël
Loywick, Alexandre
Audebert, Christophe
Hot, David
MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
title MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
title_full MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
title_fullStr MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
title_full_unstemmed MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
title_short MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
title_sort micra: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738152/
https://www.ncbi.nlm.nih.gov/pubmed/29258574
http://dx.doi.org/10.1186/s13059-017-1367-z
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