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
Puhti: 4.8.1
Usage
The setup command for CD-HIT on Puhti is:
module load biokit
After the setup command, the server recognizes CD-HIT commands. 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 |
| cd-hit | Cluster peptide sequences |
| 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 |
| cd-hit-454 | Identify duplicates from 454 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 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.fastacontains 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.clstrcontains information about the clustering of the sequences that share higher similarity than the given threshold value (in this case 95%).