Leveraging multiple transcriptome assembly methods for improved gene structure annotation [article]

Luca Venturini, Shabhonam Caim, Gemy Kaithakottil, Daniel Lee Mapleson, David Swarbreck
2017 bioRxiv   pre-print
The performance of RNA-Seq aligners and assemblers varies greatly across different organisms and experiments, and often the optimal approach is not known beforehand. Here we show that the accuracy of transcript reconstruction can be boosted by combining multiple approaches, and we present a novel algorithm to integrate multiple RNA-Seq assemblies into a coherent transcript annotation. Our algorithm can remove redundancies and select the best transcript models according to user-specified
more » ... while solving common artefacts such as erroneous transcript chimerisms. We have implemented this method in an open-source Python3 and Cython program, Mikado, available at https://github.com/lucventurini/Mikado.
doi:10.1101/216994 fatcat:uw7ymsrgjfanbkoqs5olqnwnhq