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SeqMonk

SeqMonk is a program to enable the visualization and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions.

Interactive Use

This application requires an X-Windows connection.

SeqMonk uses environment modules. Type

module load seqmonk

at the prompt. Then type

seqmonk

Environment variables set:

Usage of the seqmonk command is as follows:

            SeqMonk - A high throughput sequence visualisation tool

SYNOPSIS

  seqmonk [-m 4000]


DESCRIPTION

  SeqMonk is a graphical application for the visualisation and analysis of
  high throughput mapped read data.
    
    The options for the program as as follows:
    
    -h --help       Print this help file and exit
    
    -m --memory     Set the starting memory allocation in megabytes. Defaults
                    to 1300. Minimum allowed value is 500 and values above
                    1300 should only be set on systems running a 64-bit JRE
                        
BUGS

    Any bugs in SeqMonk should be reported either to simon.andrews@babraham.ac.uk
    or in www.bioinformatics.babraham.ac.uk/bugzilla/

When opening seqmonk, you are prompted to set the paths of temporary files, among other things. For temporary files, you might choose to use /lscratch/$SLURM_JOBID/igvtmp if --gres=lscratch:N is used in an interactive job (where N is the number GB needed for scratch space, or /scratch/$USER/igvtmp as the temporary directory, where $USER is your username. To allocate and use 20gb of memory on an interactive node, do:

sinteractive --mem 20g
module load seqmonk
seqmonk --memory 20000

Input/output for SeqMonk is menu-driven through the GUI. The screenshot below shows the example data from /fdb/seqmonk/example_seqmonk_data.smk

SeqMonk display window of example data

Documentation