CD-HIT-2D-PARA

Reference

CD-HIT-2D-PARA is a script that runs cd-hit-2d, cd-hit-est-2d in a parallel mode. It splits the input databases; runs cd-hit-2d or cd-hit-est-2d in parallel on a computer cluster; and finally merges the outputs into a single file. You can run it as you run cd-hit-2d or cd-hit-est-2d. The input is a protein or DNA/RAN dataset in fasta format and the output are two files: a fasta file of representative sequences and a text file of list of clusters.

Category

Sequence Analysis

Usage

cd-hit-para.pl -i nr -i2 swissprot -o swissprot_vs_nr -c 0.6 -n 4 --Q 20 -T "SGE" --S 2 --S2 20

Manual

    --P  program, "cd-hit-2d" or "cd-hit-est-2d",
         default "cd-hit-2d"
    --B  filename of list of hosts,
         requred unless -Q or -L option is supplied
    --L  number of cpus on local computer, default 0
         when you are not running it over a cluster, you can use
         this option to divide a big clustering jobs into small
         pieces, I suggest you just use "--L 1" unless you have
         enough RAM for each cpu
    --S  Number of segments to split 1st db into, default 2
    --S2 Number of segments to split 2nd db into, default 8
    --Q  number of jobs to submit to queue queuing system, default 0
         by default, the program use ssh mode to submit remote jobs
    --T  type of queuing system, "PBS", "SGE" are supported, default PBS
    --R  restart file, used after a crash of run
     -h  print this help

 

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