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Example scripts illustrating the use of dtool
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README.rst
bowtie2_align.sh
create_ecoli_reads_dataset.sh
create_paired_read_overlays_from_fname.py
create_reference_genome_dataset.sh
minify.sh
simple_processing.sh

README.rst

Example scripts illustrating the use of dtool

Generate an E. coli reference genome dataset:

bash create_reference_genome_dataset.sh U00096.3

The above generates the dataset Escherichia-coli-ref-genome.

Generate a E. coli reads dataset:

bash create_ecoli_reads_dataset.sh

The above generates the dataset Escherichia-coli-reads-ERR022075.

Generate a "minified" version of the reads dataset for testing out the processing script:

bash minify.sh Escherichia-coli-reads-ERR022075 .

The above generates the dataset Escherichia-coli-reads-ERR022075-minified.

Generate "overlays" to enable processing of the reads (requires the Python packages click, dtoolcore and dtool-cli):

python create_paired_read_overlays_from_fname.py Escherichia-coli-reads-ERR022075
python create_paired_read_overlays_from_fname.py Escherichia-coli-reads-ERR022075-minified

A simple processing example:

bash simple_processing.sh Escherichia-coli-reads-ERR022075-minified

A more complex processing example (requires bowtie2):

bash bowtie2_align.sh Escherichia-coli-reads-ERR022075-minified Escherichia-coli-ref-genome ./

The above generates the dataset Escherichia-coli-reads-ERR022075-minified-bowtie2-align.

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