Introduction
omicR creates fasta files, downloads genomes from NCBI using the refseq number, creates databases to run BLAST+, runs BLAST+ and filters these results to obtain the best match per sequence.
These scripts can be used to run BLAST alignment of short-read (DArTseq data) and long-read sequences (Illumina, PacBio… etc). You can use reference genomes from NCBI, genomes from your private collection, contigs, scaffolds or any other genetic sequence that you would like to use as reference.
This version is suitable for ubuntu-Linux users.
Watch the tutorial video in YouTube omicR with Graphical User Interface (~20 min) https://youtu.be/pdMio2vj-FM
You need to install the following:
a. Python V3 or latest: https://www.python.org/downloads/ with module tkinter Python3.7 or above has tkinter intalled, if not you can install it with:
sudo apt-get install python3-tk
b. Biopython: https://biopython.org/ python3.8 -m pip install biopython
c. omicR: https://github.com/BTalamantesBecerra/omicR Download the following files from GitHub: “omicR.py” and “Currito.xbm” and save them in your python working directory.
d. BLAST+ latest version: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Dowloading code:
git clone https://github.com/BTalamantesBecerra/omicR.git
Running omicR
*Alternative 1:
-Open the script “omicR.py” using the IDLE and run it.
-This will open a window where you can run the scripts.
*Alternative 2:
- Open the script from the command line. Move directories to the location where you downloaded the script and run it:
python3 omicR.py
-This will open a window where you can run the scripts.
As general practice avoid installing your software in directories such as “C://Program files/” as the space between words will cause problems.
For usage, please refer to the file "OmicR_User_guide.pdf" available in this repository.
If you use this script, please cite:
Berenice Talamantes-Becerra, Jason Carling, Arthur Georges. omicR: A tool to facilitate BLASTn alignments for sequence data, SoftwareX, Volume 14, 2021, 100702, ISSN 2352-7110, https://doi.org/10.1016/j.softx.2021.100702. Website: https://www.sciencedirect.com/science/article/pii/S2352711021000479