Degeneration of planting material due to the accumulation of viral pathogens is a problem that affects potato crops in Colombia. In order to offer alternatives for the identification of these infectious agents, an analysis platform was developed in Python, which allows to process next generation sequence data through two alignment tools, Magic-BLAST and BLAST, also including a decision algorithm that filters the results and builds a consensus with the partial and/or complete genomes of the viral pathogens that are listed as a possible health risk according to the country's authorities.
This program support single or paired-end reads from Illumina sequencing technology in FASTQ format (or fastq.gz):
@seq_ID [1]
CTCAGCTAAATACTTTGACACCNGTANNANNNN [2]
+ [3]
BBDEBDDDDHHHHFHEEEEEEEE#3AC##### [4]
FASTQ file is composed of four lines. [1] This line includes a unique ID and information such as flow cell lane information. [2] This line includes the nucleotides of the sequence. [3] A separator item (+). [4] This line includes quality values about sequences; this quality is denominated Phred Score and is described in ASCII symbols, every simbol has a respective number asociated and a higher number signifies higher acurracy of each nucleotide.
The test data (testfile_1.fastq - testfile_2.fastq) was tested on the following computer equipment:
| Operating system | Processor | RAM | Total execution time (min) |
|---|---|---|---|
| Windows 7 64-bit | Intel Core i5-2300 CPU @ 2,80 GHz | 8 GB | 9,71 |
| Windows 10 64-bit | Intel Core i5-6200U CPU @ 2,40 GHz | 4 GB | 18,77 |
| Windows 10 64-bit | Intel Core i5-8265U CPU @ 1,80 GHz | 8 GB | 14,24 |
Sequence alignment is done through Magic-BLAST and BLAST+, the algorithms for automatic execution and filtering are written in Python.
1. BLAST+
Please go to official BLAST+ page and install the correct version for you operative system. To verify that the tool works correctly, enter to the terminal or the command prompt and type:
blastnThe installation was successful if you get the following message:
BLAST query/options error : Either a BLAST database or subject sequence(s) must be specified
Please refer to the BLAST+ user manual.2. Magic-BLAST
Please go to official Magic-BLAST page and install the correct version for you operative system. To verify that the tool works correctly, enter to the terminal or the command prompt and type:
magicblastThe installation was successful if you get the following message:
BLAST query/options error : Either a BLAST database or subject sequence(s) must be specified
Please refer to the BLAST+ user manual.3. Python
Please go to official Python page and install the correct version (3.7+) for you operative system. To verify that the tool works correctly, enter to the terminal or the command prompt and type:
python --versionThe installation was successful if you get a message like:
Python 3.7 (or superior)Important: If you have a version lower than Python 3, the tool may not work correctly.
If you get an error like:
"python" is not recognized as an internal or external command, operable program or batch file.Use the same command, but instead of python try py. A third option is to try python3. If none of the previous solutions work, check the Issues section.
More important:
The following Python libraries are absolutely necessary and we recommend installing them through pip:
Python 3.4 and later include pip by default. If it is your case enter to the terminal or the command prompt and type:
python -m pip install pandaspython -m pip install Pillowpython -m pip install seabornpython -m pip install matplotlibBefore downloading the files make sure you meet the essential prerequisites, i.e. Python, BLAST+ and Magic-BLAST.
You can obtain VirusMAPPER at the following link.
Once the download is complete, locate the file in your preferred folder and unzip it; when you do this you will find the following structure:
----->VirusMAPPER.py
----->Databases (7 files)
>database_viral.tsv
>viral_refseqs.(nhr, nin, nog, nsd, nsi, nsq).
----->testfile_1.fastq
----->testfile_2.fastqNow you can continue with the next section.
The last update of the viral database was made on June, 2020.
Open the terminal or the command prompt as administrator and go to the folder where the downloaded files are located.
Help: If you want to know how to move between folders in the terminal or command prompt, check the following link.
You can access the program by writing the following line:
python VirusMAPPER.pyWait a moment while the user interface loads.
If you get an error like:
"python" is not recognized as an internal or external command, operable program or batch file.Use the same command, but instead of python try py. A third option is to try python3. If none of the previous solutions work, check the Issues section.
- Anaconda user's:
python AND py AND python3 ... is not recognized as an internal or external command, operable program or batch file.
You may have python installed through Anaconda, in this case you must open the Anaconda prompt.
Boratyn GM, Thierry-Mieg J, Thierry-Mieg D, Busby B, Madden T.L. (2019) "Magic-BLAST, an accurate RNA-seq aligner for long and short reads." BMC Bioinformatics. 2019 Jul 25;20(1):405.
Zhang Z., Schwartz S., Wagner L., & Miller W. (2000), "A greedy algorithm for aligning DNA sequences" J Comput Biol 2000; 7(1-2):203-14.
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