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cd-hit.rst

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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.

Versions

  • 4.8.1

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

Module

You can load the modules by:

module load biocontainers
module load cd-hit

Example job ~~~~~ .. warning:: 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