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

被引：0
作者：
Ségolène Caboche
Gaël Even
Alexandre Loywick
Christophe Audebert
David Hot
机构：
[1] University of Lille,
[2] CNRS,undefined
[3] Inserm,undefined
[4] CHU Lille,undefined
[5] Institut Pasteur de Lille,undefined
[6] U1019-UMR 8204-CIIL-Centre d’Infection et d’Immunité de Lille,undefined
[7] Genes Diffusion,undefined
[8] PEGASE-Biosciences,undefined
[9] Institut Pasteur de Lille,undefined
来源：
Genome Biology | / 18卷
关键词：
Bioinformatics pipeline; Comparative genomics; Microbial genome characterization; High-throughput sequencing;
D O I：
暂无
中图分类号：
学科分类号：
摘要：
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.
引用
收藏
相关论文
共 133 条
  • [11] Robinson ER(2006)A fast and symmetric DUST implementation to mask low-complexity DNA sequences J Comput Biol 13 1028-7
  • [12] Walker TM(2011)Patric: The comprehensive bacterial bioinformatics resource with a focus on human pathogenic species Infect Immun 79 4286-4
  • [13] Pallen MJ(2006)DrugBank: a comprehensive resource for in silico drug discovery and exploration Nucleic Acids Res 34 D668-3
  • [14] Goldberg B(2009)ARDB--Antibiotic Resistance Genes Database Nucleic Acids Res 37 D443-5
  • [15] Sichtig H(2012)ART: a next-generation sequencing read simulator Bioinformatics 28 593-403
  • [16] Geyer C(2015)IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data Bioinformatics 31 2870-35
  • [17] Ledeboer N(2013)QUAST: quality assessment tool for genome assemblies Bioinformatics 29 1072-24
  • [18] Weinstock GM(2001)Polymorphism of Bordetella pertussis isolates circulating for the last 10 years in France, where a single effective whole-cell vaccine has been used for more than 30 years J Clin Microbiol 39 4396-9
  • [19] Fricke WF(2006)Temporal analysis of French Bordetella pertussis isolates by comparative whole-genome hybridization Microbes Infect 8 2228-4
  • [20] Rasko D(2006)Attenuated Bordetella pertussis: new live vaccines for intranasal immunisation Vaccine 24 S2-50
12345678910