Documentation

Detailed documentation can be found at https://rbturnbull.github.io/orthoflow/

Input data

Orthoflow works from an input CSV file with information about the data sources to be used. Preparing this file is central to setting up your run. The default filename for this is input_sources.csv.

It needs the columns file, taxon_string, data_type and translation_table.

• The file column is the path to the file relative to the working directory.

• The taxon_string is the name of the taxon from which the data was obtained.

• The data_type column should be either CDS when providing a FASTA file with coding sequences, or GenBank when providing a GenBank-formatted file with CDS annotations.

• The translation_table column should have the translation table (genetic code) number for the data as given here.

Let’s look at the demonstration dataset distributed with the code: tests/test-data/input_sources.csv.

We are using a dataset of algal chloroplast genomes, some as annotated genbank files (data_type: Genbank), some as fasta files of the coding sequences (data_type: CDS). They all use the bacterial genetic code (translation_table: 11). Some of the genomes were in a single Genbank file (e.g. KY09313.gb at the top), others were fragmented across multiple files (e.g. last 4 all belonging to the same taxon).

The taxon_string column is perhaps the most important one, as these will be the names to appear in the output tree and this determines how input data gets grouped (e.g. all CDSs in the final four GenBank files will be grouped into a single taxon). In this case, we have included specimen numbers as part of the taxon string but that is optional.

Simple run

We are using the small demonstration dataset distributed with the Orthoflow in the tests/test-data subdirectory.

Go into the directory containing the input_sources.csv file and run orthoflow with default settings with these commands:

cd tests/test-data
orthoflow

By default, Orthoflow will extract the CDSs from the input files, run OrthoFinder followed by OrthoSNAP to determine orthologous genes, align them and infer a concatenated tree from the protein sequences. You can follow progress on the screen as the workflow executes and outputs are produced.

Note that the first time you run the workflow, it will be slow because it needs to download and install the software it depends on. This is a one-time thing and runs should get going much faster after.

Examining the output

Credits and Attribution

Orthoflow was created by Robert Turnbull, Jacob Steenwyk, Simon Mutch, Vinícius Salazar, Pelle Scholten and Heroen Verbruggen.

Citation details to follow.