Cd-hit

Introduction

Cd-hit is a very widely used program for clustering and comparing protein or nucleotide sequences.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/cd-hit
Home page: https://github.com/weizhongli/cdhit

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

4.8.1

BELL

4.8.1

GAUTSCHI

4.8.1

NEGISHI

4.8.1

SCHOLAR

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 -p wholenode        # Partition 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
module biocontainers cd-hit

# Your cd-hit workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers cd-hit

# Your cd-hit workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers cd-hit

# Your cd-hit workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers cd-hit

# Your cd-hit workflow...

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers cd-hit

# Your cd-hit workflow...