ViReaDB

ViReaDB is a user-friendly database for storing reference-compressed viral sequence data and computing consensus genome sequences.

Installation

ViReaDB can be installed using pip:

sudo pip install vireadb

If you are using a machine on which you lack administrative powers, ViReaDB can be installed locally using pip:

pip install --user vireadb

Dependencies

ViReaDB is a Python package that depends on the Pysam and NumPy packages.

If your read mappings are not already in the CRAM format (i.e., they are in the SAM or BAM format), you will also need to install Samtools for conversion to CRAM. If your reads are in the FASTQ format (meaning they need to be mapped to the reference genome), you will also need to install Minimap2. Both tools must be in your PATH. The Dockerfile in this repository may be helpful in setting up those tools.

Usage

Typical usage should be as follows:

1. Import the vireadb package
2. Use vireadb.create_db to create a new database, or use vireadb.load_db to load an existing database
3. Add new datasets to the database, and/or compute/query consensus sequences of items in the database

import vireadb
db = vireadb.load_db("example.db")
seq = db.get_consensus("my_sample")

Full documentation can be found at https://niemasd.github.io/ViReaDB/, and more examples can be found in the ViReaDB Wiki.

Citing ViReaDB

If you use ViReaDB in your work, please cite this GitHub repository (a manuscript is in preparation):

https://github.com/niemasd/ViReaDB