Ray Communities is a set of RayPlatform-compatible plugins that adds search
capabilities to the Ray distributed k-mer storage engine.

== Ray command ==

mpiexec -n 4 Ray \
-p s1.fastq s2.fastq \
-search NCBI-Bacteria \
-with-taxonomy \
Genome-to-Taxon.tsv \
TreeOfLife-Edges.tsv \
Taxon-Names.tsv


The directory NCBI-Bacteria/ contains one fasta file per strain/species.
Each header should be like:

>gi|225853611|ref|NC_012466.1| Streptococcus pneumoniae JJA, complete genome                                                                                                                         |

The identifiers (225853611 in this example) are used to place things in the tree of life.
The mapping from gi numbers to taxonomy numbers is done using the file
Genome-to-Taxon.tsv. The taxonomy tree edges is contained in
TreeOfLife-Edges.tsv. Finally, the name of the taxons are provided in
Taxon-Names.tsv.


For the NCBI taxonomy, see Documentation/NCBI-Taxonomy.txt


== Genome-to-Taxon.tsv ==

Each line has 2 columns (tab-separated):

	GenBankIdentifier	taxonIdentifier

Both are integers.



== TreeOfLife-Edges.tsv format ==

Each line has 2 columns (tab-separated):
	
	parentTaxonIdentifier	childTaxonIdentifier

Both are integers.



== Taxon-Names.tsv ==

Each line has 3 columns (tab-separated):

	taxonIdentifier	taxonName	taxonomicRank


taxonIdentifier is an integer
taxonName is a string
taxonomicRank is a string