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chevron_left Adapter trimming Read alignment Read quality control Bioinformatics workflows SNP/SNV annotation Venn diagram creation chevron_right
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Tool usage distribution map

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Associated diseases

Associated diseases

MICRA specifications

Information


Unique identifier OMICS_25468
Name MICRA
Alternative name Microbial Identification and Characterization through Reads Analysis
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data Some reads and the sequencing technology.
Input format FASTQ, ZIP, GZ
Biological technology Illumina
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ségolène Caboche <>

Information


Unique identifier OMICS_25468
Name MICRA
Alternative name Microbial Identification and Characterization through Reads Analysis
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Ségolène Caboche <>

Publication for Microbial Identification and Characterization through Reads Analysis

MICRA in publications

 (251)
PMCID: 5943489
PMID: 29774014
DOI: 10.3389/fmicb.2018.00862

[…] the abundance of fusobacterium increased, while the number of streptococcus, haemophilus, porphyromonas, and actinomyces decreased with cancer progression. fusobacterium periodonticum, parvimonas micra, streptococcus constellatus, haemophilus influenza, and filifactor alocis were associated with oscc, and they progressively increased in abundance from stage 1 to stage 4. the abundances […]

PMCID: 5935009
PMID: 29755482
DOI: 10.3389/fpls.2018.00420

[…] of 1 g of were ground to a fine powder with liquid nitrogen and extracted twice with 2.5 ml of 80% methanol in falcon tubes. thereafter, the samples were further homogenized by ultrasonication (micra d-9 homogenizer, art, müllheim germany) for 1 min and 15 s at 10,000 rpm. two milliliters of the methanol extracts were transferred to microtubes and centrifuged at 5,645 × g for 5 min. […]

PMCID: 5945244
PMID: 29680846
DOI: 10.4317/medoral.22238

[…] condition compared to patients without cyclosporine (p<0.05). prevalence of porphyromonas gingivalis, tannerella forsythia and fusobacterium nucleatum was reduced and prevalence of parvimonas micra and capnocytophaga species was increased in patients under immunosuppression with glucocorticoids, mycophenolate as well as combination therapy., time under and form of immunosuppression might […]

PMCID: 5932350
PMID: 29755418
DOI: 10.3389/fmicb.2018.00643

[…] of unilateral maxillary crs the genera fusobacterium, prevotella, and parvimonas were found at high abundance in the cultivation independent analysis, while in parallel f. nucleatum, parvimonas micra, and prevotalla oris, were found in the cultivation based study in high quantities. these bacteria are typical members of the oral flora and regularly cultivated from chronic periodontitis […]

PMCID: 5896039
PMID: 29642940
DOI: 10.1186/s40168-018-0451-2

[…] samples from chinese, austrian, american, and german and french cohorts, seven crc-enriched bacteria (bacteroides fragilis, fusobacterium nucleatum, porphyromonas asaccharolytica, parvimonas micra, prevotella intermedia, alistipes finegoldii, and thermanaerovibrio acidaminovorans) have been identified across populations. the seven enriched bacterial markers classified cases from controls […]


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MICRA institution(s)
University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d’Infection et d’Immunité de Lille, Lille, France; PEGASE-Biosciences, Institut Pasteur de Lille, Lille, France
MICRA funding source(s)
Supported by University of Lille, Institut Pasteur de Lille, and the Gènes Diffusion company.

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