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

Abstract 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 t...

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Main Authors:	Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert, David Hot
Format:	Article
Language:	English
Published:	BMC 2017-12-01
Series:	Genome Biology
Subjects:	Bioinformatics pipeline Comparative genomics Microbial genome characterization High-throughput sequencing
Online Access:	http://link.springer.com/article/10.1186/s13059-017-1367-z

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spelling	doaj-abfe3e1325ee49428d0da570ad3c283a2020-11-24T20:42:06ZengBMCGenome Biology1474-760X2017-12-0118111410.1186/s13059-017-1367-zMICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing dataSégolène Caboche0Gaël Even1Alexandre Loywick2Christophe Audebert3David Hot4University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d’Infection et d’Immunité de LilleGenes DiffusionGenes DiffusionGenes DiffusionUniversity of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d’Infection et d’Immunité de LilleAbstract 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.http://link.springer.com/article/10.1186/s13059-017-1367-zBioinformatics pipelineComparative genomicsMicrobial genome characterizationHigh-throughput sequencing
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Ségolène Caboche Gaël Even Alexandre Loywick Christophe Audebert David Hot
spellingShingle	Ségolène Caboche Gaël Even Alexandre Loywick Christophe Audebert David Hot MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data Genome Biology Bioinformatics pipeline Comparative genomics Microbial genome characterization High-throughput sequencing
author_facet	Ségolène Caboche Gaël Even Alexandre Loywick Christophe Audebert David Hot
author_sort	Ségolène Caboche
title	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_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_sort	micra: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
publisher	BMC
series	Genome Biology
issn	1474-760X
publishDate	2017-12-01
description	Abstract 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.
topic	Bioinformatics pipeline Comparative genomics Microbial genome characterization High-throughput sequencing
url	http://link.springer.com/article/10.1186/s13059-017-1367-z
work_keys_str_mv	AT segolenecaboche micraanautomaticpipelineforfastcharacterizationofmicrobialgenomesfromhighthroughputsequencingdata AT gaeleven micraanautomaticpipelineforfastcharacterizationofmicrobialgenomesfromhighthroughputsequencingdata AT alexandreloywick micraanautomaticpipelineforfastcharacterizationofmicrobialgenomesfromhighthroughputsequencingdata AT christopheaudebert micraanautomaticpipelineforfastcharacterizationofmicrobialgenomesfromhighthroughputsequencingdata AT davidhot micraanautomaticpipelineforfastcharacterizationofmicrobialgenomesfromhighthroughputsequencingdata
_version_	1716823159176429568

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

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