Discovery of phylogenetic markers from orthologous sequences.
If you use DiscoMark in you research, please cite:
Rutschmann S‡, Detering H‡, Simon S, Fredslund J, Monaghan MT (2016) DiscoMark: Nuclear marker discovery from orthologous sequences using draft genome data. Molecular Ecology Resources, DOI: 10.1111/1755-0998.12576. ‡, co-first authors
DiscoMark is a python script and depends on several programs. The below instructions should work well for Unix-based (Linux, Apple OS X, etc.) operation systems. It might also be possible to run the program under Windows, however this has not been tested.
DiscoMark, uses the following programs:
- Python (>= 2.7)
- NCBI Blast+ (>= 2.2.29)
- MAFFT (>= 6.864b)
- TrimAl (>= 1.4)
For Linux and Mac, we include binary files for BLASTn, MAFFT and TrimAl in the respective bin/ folders. See the Installation section on how to use them.
Additionally, you'll need the following Python packages:
- Biopython (>= 1.62)
- SqlAlchemy (>= 0.9)
To facilitate the installation of these packages, we suggest to use the python module manager pip (which normally comes with python3). To check which version is available on your computer type:
pip -V
To install the two python packages Biopython and SQLAlchemy you simply type the following:
sudo pip install biopython
sudo pip install sqlalchemy
Download DiscoMark (when setting the PATH environment variable, replace linux with mac if you're on a Mac):
git clone https://github.com/hdetering/discomark.git
export PATH=$PATH:$PWD/discomark/bin/linux
If you have the programs BLAST+, MAFFT and TrimAl installed on your system you don't need the export PATH=[...] statement. In case you want to use the provided binaries, make sure to execute the export PATH=[...] statement each time you login or make the change persistent in your user profile (works slightly different for linux and mac).
Make sure your input data is formatted as FASTA format.
Let´s say you want to discover markers for two species (i.e. species1 and species2) and use a reference (i.e. reference.fasta), you will call DiscoMark like this:
cd discomark
python run_project.py -i example/hamstr/species1 -i example/hamstr/species2 -r example/reference/reference.fasta -d output
If you want to add an annotation file for the input markers, you will call DiscoMark like this:
cd discomark
python run_project.py -i example/hamstr/species1 -i example/hamstr/species2 -r example/reference/reference.fasta -a input/co2go.ixosc.csv -d output
Under the defualt settings you will perform on online BLAST search for you primer pairs. Let´s say you do not have an internet connection or do not want to use this option you can call DiscoMark like this:
cd discomark
python run_project.py -i example/hamstr/species1 -i example/hamstr/species2 -r example/reference/reference.fasta -a input/co2go.ixosc.csv -d output --no-primer-blast
Please see the wiki for the complete information on the command line options.
An interactive HTML file in the output directory at 7_report/discomark_results.html contains all important information about the designed primer pairs.
(In the example above that would be: output/7_report/discomark_results.html.)
A table with all primer pairs is also avialable at CSV format in 7_report/primers.xls.
Notice: This program may contain errors. Please inspect results carefully.
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it under the GPLv2 conditions
Have a look at the FAQ.
If the FAQ is not helpful, you can open an issue to inform us about your problem.