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[DESCRIPTION]
<p>How to run <a href="https://ccb.jhu.edu/software/centrifuge" target="_blank" rel="noopener noreferrer">Centrifuge</a>  <a href="https://github.com/infphilo/centrifuge/releases/tag/v1.0.4-beta" target="_blank" rel="noopener noreferrer">version 1.0.4-beta</a> (<a href="https://genome.cshlp.org/content/early/2016/11/16/gr.210641.116.abstract" target="_blank" rel="noopener noreferrer">Kim <em>et al.</em> 2016</a>) through the <a href="https://www.imicrobe.us" target="_blank" rel="noopener noreferrer">iMicrobe</a> plaform.</p>
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<p><a href="http://www.ccb.jhu.edu/software/centrifuge" target="_blank" rel="noopener noreferrer">Centrifuge</a> is a microbial classification engine that enables rapid, accurate, and sensitive taxonomic labeling of metagenomic reads and quantification of species. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. </p>
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<p>More informations about centrifuge can be found here : https://ccb.jhu.edu/software/centrifuge/manual.shtml</p>

[BEFORE_START]
<ul>
<li>You need a working Cyverse account to connect to iMicrobe.<br />To explore how to log into iMicrobe, read <a href="https://www.protocols.io/view/logging-into-imicrobe-us-rmmd446" target="_blank" rel="noopener noreferrer">the dedicated protocol</a>. </li>
<li>Your dataset of interest should be metagenomic reads, in a fasta or fastq format.<br /><br /></li>
<li>In iMicrobe, there is several ways to run an app on a dataset (from the cart, from your personnal datastore and form an URL). If you need more information on how to run an app, <a href="https://www.protocols.io/view/running-an-app-on-imicrobe-r9jd94n" target="_blank" rel="noopener noreferrer">read the protocol associated</a>.</li>
</ul>

[GUIDELINES]
More informations and details about Centrifuge can be found here : https://ccb.jhu.edu/software/centrifuge/manual.shtml 
 
 
Several parameters are available to the user through the iMicrobe app. 
Index : 
Centrifuge indexes are the reference databases used for the taxonomic classification. Standard choices are all of the complete RefSeq prokaryotic, human and viral genomes, or using the sequences that are part of the NCBI nt database.
The indexes provided in iMicrobe are provided by the tool authors, available here. The updataing dates for the indeces are the following :  
Bacteria, Archea, Virus, Human : 12/06/2016
Bacteria, Archea : 4/15/2018
NCBI nt : 3/3/2018

Exclude :
A comma-separated list of taxonomic IDs that will be excluded in classification procedure. The descendants from these IDs will also be excluded. To find the taxonomic ID, one can use the NCBI taxonomic browser. 
File format :
The user can provide a Fasta or a Fastq formated file as an input. Please use the drop down menu to select to correct format for your file.
Reads are paired :
If you are working on illumina paired reads, select that option to allow the reads to be paired before their taxonomic assignment.
Figure title :
The iMicrobe Centrifuge app provides a bubble-chart representation of the result. The title of the vizualization can be changed.

[STEPS]
SECTION: Running Centrifuge on 454 datasets
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SECTION: Running Centrifuge on 454 datasets excluding E. coli and P. aeruginosa
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SECTION: Running Centrifuge on paired-end reads
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