Getting Started
Project Setup
Segminator II requires a project to be set up prior to data input. This involves entering a project name (using the "Add Project" menu option) and providing a template in FASTA format.

Adding Data
After setting up a project, datasets in FASTQ format can be added using the "Add Dataset" menu. When a dataset is added the software will generate an assembly by first mapping and then pairwise aligning each read. All additional datasets added to the project will be mapped and pairwise aligned to the same template, thus allowing for a direct comparison of the tabulated output.

Sample Data
Sample data consisting of a partial env template and some HIV-1 reads, obtained using the 454 Life Sciences, is available here.

Further Detail
Technical details of assembly generation and the data structures used to store reads are discussed in [PLoS Comput Biol. 2010 Dec 16;6(12):e1001022].