KmerGenie-Teaching

Category

Bioinformatics

Program On

Teaching

Version

1.7044

Author / Distributor

KmerGenie

Description

"KmerGenie estimates the best k-mer length for genome de novo assembly." More details are at KmerGenie

Running Program

The last version of this application is at /usr/local/apps/eb/KmerGenie/1.7044-foss-2016b

To use this version, please load the module with

ml KmerGenie/1.7044-foss-2016b 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_KmerGenie
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=KmerGenie.%j.out
#SBATCH --error=KmerGenie.%j.err

cd $SLURM_SUBMIT_DIR
ml KmerGenie/1.7044-foss-2016b
kmergenie [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml KmerGenie/1.7044-foss-2016b 
kmergenie --help
KmerGenie 1.7044

Usage:
    kmergenie <read_file> [options]

Options:
    --diploid    use the diploid model (default: haploid model)
    --one-pass   skip the second pass to estimate k at 2 bp resolution (default: two passes)
    -k <value>   largest k-mer size to consider (default: 121)
    -l <value>   smallest k-mer size to consider (default: 15)
    -s <value>   interval between consecutive kmer sizes (default: 10)
    -e <value>   k-mer sampling value (default: auto-detected to use ~200 MB memory/thread)
    -t <value>   number of threads (default: number of cores minus one)
    -o <prefix>  prefix of the output files (default: histograms)
    --debug      developer output of R scripts
    --orig-hist  legacy histogram estimation method (slower, less accurate)

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Installation

Source code is obtained from KmerGenie

System

64-bit Linux