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`