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Department of Microbiology and Immunology

Software

Open-Source Software developed in-house

Vironator

Vironator is a virus-hunting program. It uses a novel classification algorithm with Radial Distance Weighted Discrimination, to classify real-life samples as positive or negative matches. Its training stage allows it to detect non-identical but related targets, as well as detecting target within a specific background (e.g. detecting specific virus in Human with bacterial infection). Vironator is developed by Jie Xiong and Jordan Texier.

Requirements:

  • MATLAB 2013a
  • Bowtie2
  • Samtools

Downloads: TBA

(will be available to download after publication)

Prime Time

PrimeTime is our in-house software for high throughput primer design. It is available free only for academic and non-commercial uses. Any use requires attribution of the original work [Dongmei Yang, Wolfgang Vahrson and Dirk P. Dittmer – paper citation TBA]. If you want to use PrimeTime for commercial purpose, you need to license it separately from these authors. Note: No warranty or fitness of any kind is implied. This is research code!

Warning: The following code is optimized for OSX 10.5 and MySQL 5.0. These versions are now obsolete. Use with care:
Download the source code: PrimeTime version 0.1
Download the pre-built and easy-to-install package: PrimeTime Package

 Vivonatev

Vivonatev is a NGS mapping pipeline using Bowtie2 and Samtools. This pipeline can match NGS reads to large amounts of reference genomes. Features include:

  • Can map both single-end and paired-end NGS reads
  • Ability to recursively filter out each reference genome
  • Extract positively mapped reads
  • Generate coverage vector of each genome
  • Threshold for filtering and generating coverage vector (saves a lot of time)
Prerequisites: Bowtie2, Samtools, bam2fastq (from Hudson Alpha), python 2.7

Download from Github Repository: Vivonatev

Direct Download: tar.gz

Direct Download: zip