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