CD-HIT¶

CD-HIT is used for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. The cdhit bundle packages version 4.8.1.

UFS HPC Usage Example¶

The following command can be executed in the terminal to load the bundle:

1	`module load cdhit`

The CD-HIT utilities can be run as shown below:

cd-hit
cd-hit-2d
cd-hit-2d-para.pl
cd-hit-454
cd-hit-clstr_2_blm8.pl
cd-hit-div
cd-hit-div.pl
cd-hit-est
cd-hit-est-2d
cd-hit-para.pl

The cdhit_shell commmand can be used to access a shell in the cdhit bundle.

1	`cdhit_shell`

Performance Notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

UFS HPC Community Guides and Tutorials¶

No community guides available.

Official site and documentation¶

Licensing Information¶

CD-HIT is licensed under the GPLv2 license.

Primary citation¶

External Guides and Resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za