ViReaDB is a user-friendly database for storing reference-compressed viral sequence data and computing consensus genome sequences.
ViReaDB can be installed using
sudo pip install vireadb
If you are using a machine on which you lack administrative powers, ViReaDB can be installed locally using
pip install --user vireadb
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.
Typical usage should be as follows:
- Import the
vireadb.create_dbto create a new database, or use
vireadb.load_dbto load an existing database
- 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.
If you use ViReaDB in your work, please cite this GitHub repository (a manuscript is in preparation):