Main menu

Graphmap2 - splice-aware RNA-seq mapper for long reads


In this paper we present Graphmap2, a splice-aware mapper built on our previously developed DNA mapper Graphmap. Graphmap2 is tailored for long reads produced by Pacific Biosciences and Oxford Nanopore devices. It uses several newly developed algorithms which enable higher precision and recall of correctly detected transcripts and exon boundaries. We compared its performance with the state-of-the-art tools Minimap2 and Gmap. On both simulated and real datasets Graphmap2 achieves higher mappability and more correctly recognized exons and their ends. In addition we present an analysis of potential of splice aware mappers and long reads for the identification of previously unknown isoforms and even genes.

The Graphmap2 tool is publicly available at https://github.com/lbcb-sci/graphmap2.

Authors: Josip Maric, Ivan Sovic, Kresimir Krizanovic, Niranjan Nagarajan, Mile Sikic

Getting started

Buy a MinION starter pack Nanopore store Sequencing service providers Channel partners

Nanopore technology

Subscribe to Nanopore updates Resources and publications What is the Nanopore Community

About Oxford Nanopore

News Company timeline Sustainability Leadership team Media resources & contacts For investors For partners Working at Oxford Nanopore Current vacancies Commercial information BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
English flag