GraphMap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data. It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant improvement over the state-of-the-art for PacBio read mappers. It can also be used as an overlapper and has recently been upgraded for RNA mapping to transcriptome.
GraphMap was also designed for ease-of-use: the default parameters can handle a wide range of read lengths and error profiles, including: Illumina, PacBio and Oxford Nanopore. This is an especially important feature for technologies where the error rates and error profiles can vary widely across, or even within, sequencing runs.
GraphMap GitHub page: https://github.com/isovic/graphmap