GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html
Features
Mapping position agnostic to alignment parameters.
Consistently very high sensitivity and precision across different error profiles, rates and sequencing technologies even with default parameters.
Circular genome handling to resolve coverage drops near ends of the genome.
E-value.
Meaningful mapping quality.
Various alignment strategies (semiglobal bit-vector and Gotoh, anchored).
Overlapping of reads for de novo assembly.
Transcriptome mapping through internal construction of a transcriptome from a given genomic reference and a GTF file.
...and much more.
GraphMap is also used as an overlapper in a new de novo genome assembly project called Ra (https://github.com/mariokostelac/ra-integrate.
Ra attempts to create de novo assemblies from raw nanopore and PacBio reads without requiring error correction, for which a highly sensitive overlapper is required.
Currently, development of a new spliced-alignment mode for mapping RNA-seq reads is under way.
Description of the current effort as well as how to reach the experimental implementation can be found here: doc/rnaseq.md.
