RapMap is a testing ground for ideas in read mapping. That means that, at this point, it is somewhat experimental and there are no guarantees on stability / compatibility between commits. Currently, RapMap is a stand-alone quasi-mapper (and pseudo-aligner) 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.
Lightweight-alignment / quasi-mapping / pseudo-alignment is the term I'm using 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-to-base CIGAR string that aligns the read and substring of the transcript. For details on RapMap (quasi-mapping in particular), please check out the pre-print on bioRxiv. Note: while RapMap implements both quasi-mapping and pseudo-alignment, these two are not the same thing --- quasi-mapping is not pseudo-alignment, or an algorithm for obtaining pseudo-alignments. Quasi-mapping and pseudo-alignment are distinct concepts, and RapMap simply happens to implement both.
There are a number of different ways to collect such information, and the idea of RapMap (as the repository grows) will be to explore multiple different strategies in how to most rapidly determine all feasible / compatible locations for a read within the transcriptome. In this sense, it is like an all-mapper; the alignments it outputs are intended to be (eventually) disambiguated (Really, it's more like an "all-best" mapper, since it returns all hits in the top "stratum" of lightweight/quasi/pseudo mappings). If there is a need for it, best-mapper functionality may be added in the future.
To build RapMap, you need a C++11 compliant compiler (g++ >= 4.7 and clang >= 3.4) and CMake. RapMap is built with the following steps (assuming that path_to_rapmap is the toplevel directory where you have cloned this repository):
[path_to_rapmap] > mkdir build && cd build
[path_to_rapmap/build] > cmake ..
[path_to_rapmap/build] > make
[path_to_rapmap/build] > make install
[path_to_rapmap/build] > cd ../bin
[path_to_rapmap/bin] > ./rapmap -h
This should output the standard help message for rapmap.
No, at least not right now. The index and mapping strategy employed by RapMap are highly geared toward mapping to transcriptomes. It may be the case that some of these ideas can be successfully applied to genomic alignment, but this functionality is not currently suppored (and is not a high priority right now).
RapMap is very fast --- hence the name. On a synthetic test dataset comprised of 75 million 76bp paired-end reads, mapping to a human transcriptome with ~213,000 transcripts, RapMap takes ~ 10 minutes to align all of the reads on a single core (on an Intel Xeon E5-2690 @ 3.00 GHz) --- if you actually want to write out the alignments --- it depends on you disk speed, but for us it's ~15 minutes. Again, these mapping times are on a single core, and significant optimizations are still possible --- but RapMap is trivially parallelizable and can already be run with multiple threads.
Yes, in testing on synthetic data from multiple simulators, we find RapMap to be highly accurate. Moreover, when comparing RapMap against more traditional aligners, we find that it gives highly-concordant results. For more details, please check out the pre-print.
RapMap is experimental, and the code, at this point, is subject to me testing out new ideas. This also means that little effort has been put into size or speed optimizaiton (but it's already very fast --- see above). There are numerous ways that the code can be sped up and the memory footprint reduced, but that hasn't been the focus yet --- it will be eventualy. All of this being said --- RapMap is open to the community because I'd like feedback / help / thoughts. So, if you're not scared off by any of the above, dig in!
Since RapMap uses Jellyfish, it must be released under the GPL. However, this is currently the only GPL dependency. If it can be replaced, I'd like to re-license RapMap under the BSD license. I'd be happy to accept pull-requests that replace the Jellyfish components with a library released under a more liberal license (BSD-compatible), but note that I will not accept such pull requests if they reduce the speed or increase the memory consumption over the Jellyfish-based version.