Applications/Centrifuge - Revision history

Pysdlb: /* Batch Job */

2022-11-17T09:50:13Z

‎Batch Job

Pysdlb at 09:45, 17 November 2022

2022-11-17T09:45:48Z

Pysdlb: /* Usage Examples */

2022-11-17T09:31:30Z

‎Usage Examples

Pysdlb: /* Navigation */

2022-11-16T10:39:17Z

‎Navigation

Pysdlb at 09:29, 23 August 2022

2022-08-23T09:29:06Z

Pysdlb at 09:26, 23 August 2022

2022-08-23T09:26:44Z

Pysdlb at 11:16, 24 May 2019

2019-05-24T11:16:46Z

Chris.collins: Created page with "TOC ==Application Details== * Description: Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantif..."

2019-01-24T09:36:45Z

Created page with "__TOC__ ==Application Details== * Description: Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantif..."

New page

__TOC__

==Application Details==

* Description: Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species.
* Version: 1.0.4
* Modules: centrifuge/1.0.4
* Licence: Open source (Github)

==Usage Examples==

[Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[username@login01 ~]$ module add centrifuge/1.0.4

</pre>

==Further Information==

* [https://github.com/infphilo/centrifuge https://github.com/infphilo/centrifuge]

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

@@ Line 35: / Line 35: @@
 #!/bin/bash
-#SBATCH -J abyss
+#SBATCH -J centrifuge
-#SBATCH -p highmem
+#SBATCH -p compute
 #SBATCH -o %N.%j.%a.out
 #SBATCH -e %N.%j.%a.err
 #SBATCH --exclusive
-#SBATCH -t 00:30:00
+#SBATCH -t 00:10:00
 module purge

← Older revision		Revision as of 09:45, 17 November 2022
Line 29:		Line 29:
	[username@login01 ~]$ module add centrifuge/1.0.4a		[username@login01 ~]$ module add centrifuge/1.0.4a

		+	</pre>
		+
		+	===Batch Job===
		+	<pre>
		+	#!/bin/bash
		+
		+	#SBATCH -J abyss
		+	#SBATCH -p highmem
		+	#SBATCH -N 2
		+	#SBATCH --ntasks-per-node=40
		+	#SBATCH -o %N.%j.%a.out
		+	#SBATCH -e %N.%j.%a.err
		+	#SBATCH -p highmem
		+	#SBATCH --exclusive
		+	#SBATCH -t 00:30:00
		+
		+	module purge
		+	module load centrifuge/1.0.4
		+
		+	###Run your commands###
		+	centrifuge-download -o library -d "vertebrate_mammalian" -a "Chromosome" -t 9606,10090 -c 'reference genome' >> seqid2taxid.map
		+	#etc...
	</pre>		</pre>

@@ Line 14: / Line 14: @@
 * The Centrifuge homepage is http://www.ccb.jhu.edu/software/centrifuge
 * The Centrifuge paper is available at https://genome.cshlp.org/content/26/12/1721
-* The Centrifuge poster is available at http://www.ccb.jhu.edu/people/infphilo/data/Centrifuge-poster.pdf
+<!--* The Centrifuge poster is available at http://www.ccb.jhu.edu/people/infphilo/data/Centrifuge-poster.pdf-->

← Older revision		Revision as of 10:39, 16 November 2022
Line 35:		Line 35:
	* [https://github.com/infphilo/centrifuge https://github.com/infphilo/centrifuge]		* [https://github.com/infphilo/centrifuge https://github.com/infphilo/centrifuge]

−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 10: / Line 10: @@
 ==Usage Examples==
-[Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at a very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers
+[Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome). It classifies sequences at a very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers
 centrifuge (1.0.4) is the main GitHub repo with 1.0.4a as the patched version according to

@@ Line 3: / Line 3: @@
 ==Application Details==
-* Description: Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species.
+* Description: Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species.
-* Version: 1.0.4
+* Version: 1.0.4 (and 1.0.4a see text below)
-* Modules: centrifuge/1.0.4
+* Modules: centrifuge/1.0.4 and centrifuge/1.0.4a
 * Licence: Open source (Github)
 ==Usage Examples==
-[Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers
+[Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at a very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 [username@login01 ~]$ module add centrifuge/1.0.4
 </pre>

@@ Line 22: / Line 22: @@
 * [https://github.com/infphilo/centrifuge https://github.com/infphilo/centrifuge]
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]