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Blobtools

Blobtools is a Bioinformatics application that provides a modular command-line solution for analysis of genome data sets.

Blobtools is available as a module on Apocrita.

Usage

To run the latest installed version of Blobtools, simply load the blobtools module:

module load blobtools
$ blobtools -h
usage: blobtools <command> [<args>...] [--help] [--version]

commands:

    create        create a BlobDB
    view          print BlobDB as a table
    blobplot      plot BlobDB as a blobplot
    covplot       compare BlobDB cov(s) to additional cov file

    map2cov       generate cov file from bam file
    seqfilter     filter FASTA sequences based on header in list
    taxify        assign taxids to blast-results based on list
    bamfilter     filter reads in a BAM file

    -h, --help      show this
    -v, --version   show version number

See 'blobtools <command> --help' for more information on a specific command.

examples:

    # Create a BlobDB
    ./blobtools create -i test.fna -b test.bam -t test.blast.out -o test

    # Generate a tabular view
    ./blobtools view -i test.blobDB.json

    # Generate a blobplot
    ./blobtools blobplot -i test.blobDB.json

Example job

Core Usage

The bamfilter module has a --threads option. If you use this module you should use: --threads ${NSLOTS} to ensure your workload uses the resources you have requested.

Serial job

Here is an example job running on 4 cores:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load blobtools
blobtools create -i assembly.fna \
                 -b mapping_1.bam \
                 -t blast.out \
                 -o my_first_blobplot

References