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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

CD-HIT

CD-HIT can be used for clustering large sequence sets or removing identical or highly similar sequences from a sequence set. CD-HIT is often used as a tool to produce a non-redundant sequence set for further analysis of a large sequence set. CD-HIT recognizes fasta and fastq sequence formats.

License

Free to use and open source under GNU GPLv2.

Available

  • Roihu: 4.8.1 (module cdhit), via the bio-apps module.

Usage

CD-HIT is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the CD-HIT module:

module load bio-apps/v202603
module load cdhit/4.8.1

After loading, the CD-HIT commands are available. The CD-HIT package has many programs. The most notable are:

Program Description
cd-hit Clustering and redundancy removal tool for protein sequences
cd-hit-est Clustering and redundancy removal tool for nucleic acid sequences (only for sequences that do not contain introns)
cd-hit-2d Tool to compare two protein sequence sets
cd-hit-est-2d Tool to compare two nucleic sequence sets
cd-hit-454 A program to identify artificial duplicates from raw 454 sequencing reads
psi-cd-hit Cluster proteins at less than 40% cutoff
cd-hit-lap Identify overlapping reads
cd-hit-dup Identify duplicates from single or paired Illumina reads
h-cd-hit Hierarchical clustering

A full list of programs can be found in the CD-HIT user guide.

You can list the command line options of CD-HIT programs by using the option -help. For example:

cd-hit -help

A simple analysis of a protein sequence set can be done, for example, with the command:

cd-hit -i my_proteins.fasta -o reduced_set.fasta -c 0.95

The sample command above produces two result files:

  • reduced_set.fasta contains a pruned sequence set. In this case, if two sequences are more than 95% identical, only the longer one is included in the results.
  • reduced_set.fasta.clstr contains information about the clustering of the sequences that share higher similarity than the given threshold value (in this case 95%).

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