cd-hit
Link to section 'Introduction' of 'cd-hit' Introduction
Cd-hit is a very widely used program for clustering and comparing protein or nucleotide sequences.
For more information, please check its website: https://biocontainers.pro/tools/cd-hit and its home page on Github.
Link to section 'Versions' of 'cd-hit' Versions
- 4.8.1
Link to section 'Commands' of 'cd-hit' Commands
- FET.pl
- 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
- clstr2tree.pl
- clstr2txt.pl
- clstr2xml.pl
- clstr_cut.pl
- clstr_list.pl
- clstr_list_sort.pl
- clstr_merge.pl
- clstr_merge_noorder.pl
- clstr_quality_eval.pl
- clstr_quality_eval_by_link.pl
- clstr_reduce.pl
- clstr_renumber.pl
- clstr_rep.pl
- clstr_reps_faa_rev.pl
- clstr_rev.pl
- clstr_select.pl
- clstr_select_rep.pl
- clstr_size_histogram.pl
- clstr_size_stat.pl
- clstr_sort_by.pl
- clstr_sort_prot_by.pl
- clstr_sql_tbl.pl
- clstr_sql_tbl_sort.pl
- make_multi_seq.pl
- plot_2d.pl
- plot_len1.pl
Link to section 'Module' of 'cd-hit' Module
You can load the modules by:
module load biocontainers
module load cd-hit
Link to section 'Example job' of 'cd-hit' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Cd-hit on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=cd-hit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers cd-hit
cd-hit -i Cm_pep.fasta -o Cmdb90 -c 0.9 -n 5 -M 16000 -T 8
cd-hit-est -i Cm_dna.fasta -o Cmdb90_nt -c 0.9 -n 5 -M 16000 -T 8