title: Manananggal - a novel viewer for alternative splicing events.
abstract: BACKGROUND
  Alternative splicing is an important cellular mechanism that can be analyzed by RNA sequencing. However, identification of splicing events in an automated fashion is error-prone. Thus, further validation is required to select reliable instances of alternative splicing events (ASEs). There are only few tools specifically designed for interactive inspection of ASEs and available visualization approaches can be significantly improved.
  
  
  RESULTS
  Here, we present Manananggal, an application specifically designed for the identification of splicing events in next generation sequencing data. Manananggal includes a web application for visual inspection and a command line tool that allows for ASE detection. We compare the sashimi plots available in the IGV Viewer, the DEXSeq splicing plots and SpliceSeq to the Manananggal interface and discuss the advantages and drawbacks of these tools. We show that sashimi plots (such as those used by the IGV Viewer and SpliceSeq) offer a practical solution for simple ASEs, but also indicate short-comings for highly complex genes.
  
  
  CONCLUSIONS
  Manananggal is an interactive web application that offers functions specifically tailored to the identification of alternative splicing events that other tools are lacking. The ability to select a subset of isoforms allows an easier interpretation of complex alternative splicing events. In contrast to SpliceSeq and the DEXSeq splicing plot, Manananggal does not obscure the gene structure by showing full transcript models that makes it easier to determine which isoforms are expressed and which are not.
authors.affiliation: Roche Pharma Research & Early Development, Roche Innovation Center Munich, Nonnenwald 2, 82377, Penzberg, Germany.
authors.forename: Matthias
authors.identifier: http://orcid.org/0000-0002-6535-0533
authors.initials: M
authors.lastname: Barann
authors.affiliation: Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 17, D-80333, Munich, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
authors.affiliation: Roche Pharma Research & Early Development, Roche Innovation Center Basel, Grenzacherstraße 124, 4052, Basel, Switzerland. fabian.birzele@roche.com.
authors.forename: Fabian
authors.initials: F
authors.lastname: Birzele
mesh_terms: D017398:Alternative Splicing; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020407:Internet; D059368:RNA Isoforms / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D059368:RNA Isoforms
keywords: Alternative splicing; RNASeq; Visualization; Web application