Difference between revisions of "CD-HIT"
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== Introduction == | == 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 == | == Installed Version == | ||
The following versions are installed and currently available... <br/> | |||
... on environment ''hpc-env/8.3'': | |||
*'''CD-HIT/4.8.1'''-GCC-8.3.0 | |||
*'''CD-HIT/4.8.1'''-iccifort-2019b | |||
... on environment ''hpc-uniol-env'' | |||
*'''CD-HIT/4.6.4''' | |||
== Using CD-HIT with the HPC Cluster == | |||
If you want to find out more about CD-HIT 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 == | == Documentation == | ||
The project page can be found [http://weizhongli-lab.org/cd-hit/ here]. | |||
Although, the most recent information can be found on [https://github.com/weizhongli/cdhit github] since the project moved there. | |||
Latest revision as of 13:40, 9 September 2021
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 following versions are installed and currently available...
... on environment hpc-env/8.3:
- CD-HIT/4.8.1-GCC-8.3.0
- CD-HIT/4.8.1-iccifort-2019b
... on environment hpc-uniol-env
- CD-HIT/4.6.4
Using CD-HIT with the HPC Cluster
If you want to find out more about CD-HIT 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 project page can be found here. Although, the most recent information can be found on github since the project moved there.
