Chromosomer-Teaching

Category

Bioinformatics

Program On

Teaching

Version

0.1.4a

Author / Distributor

Chromosomer

Description

" Chromosomer is a reference-assisted assembly tool for producing draft chromosome sequences. It provides the following routines:" More details are at Chromosomer

Running Program

The last version of this application is at /usr/local/apps/gb/chromosomer/0.1.4a

To use this version, please load the module with

ml chromosomer/0.1.4a 

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

#!/bin/bash
#SBATCH --job-name=j_Chromosomer
#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=Chromosomer.%j.out
#SBATCH --error=Chromosomer.%j.err

cd $SLURM_SUBMIT_DIR
ml chromosomer/0.1.4a
chromosomer [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 chromosomer/0.1.4a 
chromosomer  -h
usage: chromosomer [-h] [-v] [-d]
                   {assemble,fragmentmap,fragmentmapstat,fragmentmapbed,transfer,fastalength,simulator,agp2map}
                   ...

Reference-assisted chromosome assembly tool.

positional arguments:
  {assemble,fragmentmap,fragmentmapstat,fragmentmapbed,transfer,fastalength,simulator,agp2map}
    assemble            get sequences of assembled chromosomes
    fragmentmap         construct a fragment map from alignments
    fragmentmapstat     show fragment map statistics
    fragmentmapbed      convert a fragment map to the BED format
    transfer            transfer annotated features from fragments to
                        chromosomes
    fastalength         get lengths of sequences from a FASTA file
    simulator           fragment simulator for testing purposes
    agp2map             convert an AGP file to a fragment map

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -d, --debug           show debugging messages

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Installation

Source code is obtained from Chromosomer

System

64-bit Linux