Usage

Minimal example: ribo run

The pseudogenome was constructed from the 7 rDNAs separated by several kb of flanking DNA. If can be found under ./riboSeed/integration_test/concatenated_seq.fasta. If you have installed using setuptools, the integration_test folder will be installed in the site-packages dir, such as /venv-riboSeed/lib/python3.5/site-packages/riboSeed/integration_data/.

Two read files can be found in the same directory.

To run the whole riboSeed pipline, use the following command:

ribo run ./riboSeed/integration_data/concatenated_seq.fasta \
          -F ./riboSeed/integration_data/test_reads1.fq \
          -R ./riboSeed/integration_data/test_reads2.fq \
          -o ./test1/ -v 1

Whats going on:

ribo run is used to run the pipeline with the most commonly used settings. It first creates a config file, tracking down your system executables for the required tools, and setting the default parameters for things not specified as args to run_riboSeed.

Then, ribo scan is run to re-annotate your reference, ribo select calls the rDNA operons, and ribo seed runs the de fere novo assembly.

If you want to change the behaviour of the programs under the hood, all of the command line options not set by ribo run are defined in the config file in the output directory. After editing the parameters in the config file, you can submit it to ribo run using the -c flag.

Running individual scripts

All of the elements of the package can be run individually: Perhaps you want to modify barrnap’s behaviour in scan, or you want to experiment with different feature selectors in select. Go for it!

$ ribo

Description: A suite of tools to perform de fere novo assembly to bridge
gaps caused by rDNA repeats

Usage:   ribo <command> [options]

Available commands:
-run        execute pipeline (scan, select, seed, sketch, and score)
-scan       reannotate rRNAs in a FASTA file
-select     group rRNA annotations into rDNA operons
-seed       perform de fere novo assembly
-snag       extract rDNA regions and plot entropy
-sim        perform simulations used in manuscript
-sketch     plot results from a de fere novo assembly
-stack      compare coverage depth in rDNA regions to rest of genome
-score      score batches of assemblies with BLASTn
-swap       swap contigs from assemblies
-spec       use assembly graph to speculate number of rDNAs
-structure  view the rRNA operon structure across several genomes
-config     write out a blank config file to be used with `run`