Difference between revisions of "CD-HIT"
| Line 7: | Line 7: | ||
The currently installed version is 4.6.4. | The currently installed version is 4.6.4. | ||
== Using | == Using CD-HIT with the HPC Cluster == | ||
If you want to find out more about BLAT on the HPC Cluster, you can use the command | If you want to find out more about BLAT on the HPC Cluster, you can use the command | ||
module spider | module spider cd-hit | ||
This will show you basic informations e.g. a short description and the currently installed version. | This will show you basic informations e.g. a short description and the currently installed version. | ||
| Line 17: | Line 17: | ||
To load the desired version of the module, use the command, e.g. | To load the desired version of the module, use the command, e.g. | ||
module load | module load CD-HIT/4.6.4-foss-2016b-2015-0603 | ||
Always remember: this command is case sensitive! | Always remember: this command is case sensitive! | ||
After loading the module, you can run | After loading the module, you can run CD-HIT by using following command | ||
cd-hit [Options] | |||
== Documentation == | == Documentation == | ||
The full documentation can be found [http://weizhong-lab.ucsd.edu/cd-hit/ here]. | The full documentation can be found [http://weizhong-lab.ucsd.edu/cd-hit/ here]. | ||
Revision as of 14:55, 17 January 2017
Introduction
CD-HIT was originally a protein clustering program. The main advantage of this program is its ultra-fast speed. It can be hundreds of times than other clustering programs, for example BLASTCLUST. Therefore it can handle very large databases, like NR. The first version was released in 2001, the second version was publishes in 2002 with significant improvements. Since 2004 its hosted at bioinformatics.org as an open source project which helped to develop the program even more. Its still under active development and there will be new features and programs out in the future.
Installed Version
The currently installed version is 4.6.4.
Using CD-HIT with the HPC Cluster
If you want to find out more about BLAT on the HPC Cluster, you can use the command
module spider cd-hit
This will show you basic informations e.g. a short description and the currently installed version.
To load the desired version of the module, use the command, e.g.
module load CD-HIT/4.6.4-foss-2016b-2015-0603
Always remember: this command is case sensitive!
After loading the module, you can run CD-HIT by using following command
cd-hit [Options]
Documentation
The full documentation can be found here.
