olivar 0.0.1

Olivar pipeline

Olivar

Olivar is an open source pipeline for comprehensive design of primer and probe sets for pathogen sequences. Our pipeline relies on the state-of-the-art primer generating software, and incorporates low frequency variant information to ensure robust sensitivity and specificity for rapidly evolving pathogens. Additionally, our software provides visualization and validation capabilities to aid fast evaluation of the output probe and primer sets.

Install

To use Olivar, simply clone the repository and ensure that the requrements below are installed and in the system path.

Requirements

• Biopython
• Pandas
• Jinja2
• Parsnp
• Primer3
• Blast
• MAFFT
• PyVCF
• pysam

Additional requirements for simulation

1. Samtools
2. Minimap2
3. Bowtie2
4. Lofreq

Usage

To run Olivar and generate probes and primers for a set of sequences and a reference,

olivar /path/to/reference.fasta /path/to/input_genomes/ --email <your_email>

If you have a set of read datasets you'd like to use to simulate more input data:

olivar /path/to/reference.fasta /path/to/input_genomes/ \
    --simulate /path/to/read_directories
    --csv      /path/to/read_metadata.csv
    --email <your_email>

NCBI may throttle your blast queries if you only provide your email. If you have an API, you can provide that instead to have a higher allowance. Alternatively, you can supply a local blast database location via --blastdb <database_location>.

You can skip the generation of primers by adding the --probes-only flag. Please see the --help documentation for more arguments.

Output

The final output reports are present in output/final_report. In output, intermediate directories for the other modules' output is present as well.