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Welcome to VirA and BIOA’s documentation!

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VirA: Viral Quasispecies Assembler (MaxBandwidth and AmpMCF tool)

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Installation and use requires Python 2.7.

If setuptools and pip are installed, BIOA (along with VirA) can be installed simply by:

sudo pip bioa

Otherwise BIOA (and VirA) may be downloaded from bitbucket. Once downloaded and unpacked enter the new bioa directory and install by issuing the command:

sudo python install

Either mechanism for installation checks if the required Python packages are installed:

The installer will download and fetch any required packages [1]. If fetching a missing packages fails, manual installation via the above links should correct it. Note: Due to Cython and PySam only being able to run in linux environments, VirA and some BIOA functionality are limited to linux. This may change in a future version if possible.

Once installation is complete, VirA may be launched simply by:

vira read_file reference_file primer_file

VirA requires InDelFixer to align reads and kGEM to correct sequencing errors. Place the jar files for both applications in the directory you wish to run VirA in. If these tools are already installed on your system export the JAR paths to the following environment variables: INDELFIXER_PATH and KGEM_PATH. For example, if both JAR files are located in /home/jdoe/myjars/ then issue the following commands:

export INDELFIXER_PATH=/home/jdoe/myjars/


export KGEM_PATH=/home/jdoe/myjars/

Alternatively you could place these commands in your .bashrc file. Finally VirA uses SamTools for pre-processing of the sam/bam alignment files.

Using BIOA as a package in your own Python-based projects is as simple as adding:

import bioa

Installation Footnote

[1]The only exception is the CPLEX library. That is needed only for multi-commodity flow (parameter k > 0) and several algorithms. As CPLEX is proprietary software, the downloader cannot install it on required machines.