Hi,
Ray does not use any intermediate file.
You can ask Ray to write some files though.
The algorithms in Ray are quite different from other assemblers, because
Ray does no simplification to the graph.
The thing is that Ray never try to simplifies the de Bruijn graph so
there is no such thing as 'reduced nodes' in Ray like in Velvet.
Ray computes paths in the de Bruijn graph without any change to the
graph. To do so, the reads are marked in the graph and pairs are
utilised too.
One thing you can do is ask Ray to dump the whole graph with -write-kmers.
-write-kmers
Writes k-mer graph to RayOutput/kmers.txt
The resulting file is not utilised by Ray.
The resulting file is very large.
Unlike LastGraph, the resulting file is very large, however.
You can then thread the contig onto this graph.
The parts of the graph owned by each processor core can also be written
to binary files as checkpoints. However, this format is really primarily
for checkpointing and the format, while simple, is binary.
-write-checkpoints checkpointDirectory
Write checkpoint files
Are you trying to generate a proximity map ?
If so, you may want to take a look at the plugin GenomeNeighbourhood,
which is currently not enabled owing to a lack of testing.
~/git-clones/ray/code/plugin_GenomeNeighbourhood/
At the moment, the code of this plugin works, but is often stuck in
loops generated by repeated k-mers.
The ultimate goal of this plugin is to generate proximity maps, that is
something like
contig A is either before contig B or before contig B.
Then, presumably, by using brute-force combinatorial optimization, the
real order may be inferred in some cases.
- Sébastien Boisvert
Should you work on the Ray code, feel free to submit patches or pull
requests.
~/git-clones/ray/Documentation/Submit-a-patch.txt (24 lines)
~/git-clones/ray/Documentation/CodingStyle.txt (26 lines)
Mitchell Sullivan a écrit :
> Hi Sebastien,
>
> I am writing a tool that traverses the graph file in assemblies, I
> currently have it working for velvet, but as the majority of my lab
> are now using RAY, I was wondering if RAY outputs anything similar to
> the LastGraph file in velvet. i.e. a file that tells you which
> contigs/nodes are adjacent to each other.
>
> Regards,
>
> Mitchell
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