VTBuilder is a tool for the inference of non-chimeric contigs from read data that has been sequenced from complex multi-isoformic transcriptomes, such as snake venom glands, or rapidly evolving viral populations, such as HIV-1. The inference of non-chimeric sequences is of importance when studying evolution, as within chimeric sequences evolutionary relationships between co-evolving sites, functional motifs and other evolutionary factors are not maintained.
The software, which implements a six step pipeline combining aspects of both de novo and reference based assembly, has been developed by John Archer and Simon Wagstaff as part of a project funded by The Leverhulme Trust (project grant: RPG-377). The overall aim is to firstly broadly capture diversity within the data by building a set of guide sequences and then to use these guides as templates to assist in the more accurate assembly of non-chimeric transcripts. A complete description of the software is available in our manuscript.
Download and Installation
We're currently testing a new jar. Please contact Simon Wagstaff for the latest version
The simulated reads described in case study 1 that is presented in our manuscript are available in the attachment below.