In the paper
Lin, Y. et al. Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics 27, 2031–2037 (2011).
Ray is not mentioned.
Why is that so ?
We have been working on Ray for quite a while with an early prototype of the assembly engine called OpenAssembler (started in 2009-01-21).
We published Ray in 2010 in Journal of Computational Biology.
We have also presented Ray at a few places.
Cool facts about Ray:
- We are participating to Assemblathon 2.
- We assembled a genome on 512 compute cores in 18 hours, there were > 3 000 000 000 Illumina TruSeq paired reads (that is a lot of reads !)
- Ray is an high-performance peer-to-peer assembler
- Can assemble mixtures of technologies
- Is open source, licensed with the GNU GPL
- Ray is free.
- Works on POSIX systems (Linux, Mac, and others) and on Microsoft Windows
- Compiles cleanly with gcc and with Microsoft Visual Studio
- Ray utilises the message-passing interface
- Works well with Open-MPI or MPICH2 -- the 2 main open source implementations of the MPI standard.
- Ray does very few assembly errors.
- Ray is a single executable called Ray
- Implemented in C++
- Ray is object-oriented
- Ray is modular
- Ray is scalable
- Ray is easy to use.
- All the code is on github
I think the paper should have compared Ray with the other assemblers...