rapid sensitive and accurate DNA read mapping via quasi-mapping

 RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
 pseudo) transcriptome alignment. That means that, at this point, it is
 somewhat experimental. The develop branch will have the latest
 improvements and additions, but is not guaranteed to be stable between
 commits. Breaking changes to the master branch will be accompanied by a
 tag to the version before the breaking change. Currently, RapMap is a
 stand-alone quasi-mapper that can be used with other tools. It is also
 being used as part of Sailfish and Salmon. Eventually, the hope is to
 create and stabilize an API so that it can be used as a library from
 other tools.
 .
 Quasi-mapping / (lightweight / pseudo)-alignment is the term that is
 used here for the type of information required for certain tasks (e.g.
 transcript quantification) that is less "heavyweight" than what is
 provided by traditional alignment. For example, one may only need to
 know the transcripts / contigs to which a read aligns and, perhaps, the
 position within those transcripts rather than the optimal alignment and
 base-for-base CIGAR string that aligns the read and substring of the
 transcript. For details on RapMap (quasi-mapping in particular), please
 check out the associated paper. Note: RapMap implements both quasi-
 mapping and pseudo-alignment (originally introduced in Bray et al.
 2016), these two are not the same thing. They are distinct concepts, and
 RapMap simply happens to implement algorithms for computing both.