From the casper home page:

CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.

• Home page

• Module Name: casper (see the modules page for more information)
• casper is a multithreaded application. Make sure to match the number of cpus requested with the number of threads.
• Example files in $CASPER_TEST_DATA

Allocate an interactive session and run the program. Sample session:

biowulf$ sinteractive --cpus-per-task=4
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ module load casper
[user@cn3144]$ # 100nt paired end reads from fragments sized between 160 and 190 nts
[user@cn3144]$ # so they all overlapi (simulated data)
[user@cn3144]$ cp -r $CASPER_TEST_DATA/A4 .
[user@cn3144]$ ls -lh A4
total 424M
-rw-rw-r-- 1 user group 211M Feb 13  2014 A4_1.fastq
-rw-rw-r-- 1 user group 211M Feb 13  2014 A4_2.fastq
-rw-rw-r-- 1 user group 4.1K Feb 13  2014 A4_reference.fasta
-rw-rw-r-- 1 user group  413 Feb 13  2014 README

[user@cn3144]$ casper -t 4 -o A4 A4/A4_1.fastq A4/A4_2.fastq
=============================================================================
[CASPER] Context-Aware Scheme for Paired-End Read

  Input Files
     -  Forward file     : A4/A4_1.fastq
     -  Reverse file     : A4/A4_2.fastq

  Parameters
     -  Number of threads for parallel processing : 4
     -  K-mer size                                : 17
     -  Threshold for difference of quality score : 19
     -  Threshold for mismatching ratio           : 0.5
     -  Minimum length of overlap                 : 10
     -  Using Jellyfish                           : true

  K-mers : Jellyfish
     -  jellyfish count -m 17 -L 2 -o A4jellykmer -c 3 -s 10M -t 4 A4/A4_1.fastq
     -  jellyfish count -m 17 -L 2 -o A4jellykmer -c 3 -s 10M -t 4 A4/A4_2.fastq

  Output Files
     -  Merged output file            : A4.fastq

  Merging Result Statistics
     -  Total number of reads     :    1000000
     -  Number of merged reads    :     999936 (99.99%)
     -  Number of unmerged reads  :         64 (0.01%)
     -  TIME for total processing :     35.592 sec
=============================================================================
[user@cn3144]$ # creates output file A4.fastq
[user@cn3144]$ ls -lh
total 358M
drwxrwsr-x 2 user group 4.0K Feb 13  2014 A4
-rw-r--r-- 1 user group 357M Mar 22 09:21 A4.fastq
[user@cn3144]$ exit
[user@biowulf]$

Create a batch input file (e.g. casper.sh), which uses the input file 'casper.in'. For example:

#! /bin/bash

module load casper/0.8.2 || exit 1
casper -t $SLURM_CPUS_PER_TASK -w 15 -k 20 \
    -o A4 A4/A4_1.fastq A4/A4_2.fastq

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=6g casper.sh

Create a swarmfile (e.g. casper.swarm). For example:

casper -t $SLURM_CPUS_PER_TASK -w 15 -k 20 -o sample1 sample1/sample1_1.fastq sample1/sample1_2.fastq
casper -t $SLURM_CPUS_PER_TASK -w 15 -k 20 -o sample2 sample2/sample2_1.fastq sample2/sample2_2.fastq
casper -t $SLURM_CPUS_PER_TASK -w 15 -k 20 -o sample3 sample3/sample3_1.fastq sample3/sample3_2.fastq

Submit this job using the swarm command.

swarm -f casper.swarm -g 6 -t 4 --module casper/0.8.2