== Input files ==

This files can be obtained from:

	ftp://ftp.ncbi.nih.gov/pub/taxonomy/

The tree file has to be converted from Newick to simplier format (see below).

This script can do the job: https://github.com/sebhtml/NGS-Pipelines/blob/master/Phylogeny/NewickToEdges.py

== Ray command ==


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


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.




== 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

== Taxons.tsv ==

each line has 3 columns (tab-separated):

	taxonIdentifier	taxonName


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