With Ray, you can generate biological abundances.
This is done by providing Ray with a set of reference fasta sequences.
Ray Communities will use them to color the k-mers in the graph.



For example, let's say we have 1_1.fastq and 1_2.fastq containing a lot of sequences
from a given microbiome. To get the biological abundances of all NCBI viruses and
all NCBI bacteria as well as identified contigs, you can use Ray for that.

For any species that you want to check in your sample, you need to provide a single fasta
file. This file can contain chromosomes, genes, or both.

Now, you need a directory containing all viruses in fasta format (one virus per file) and
another directory containing all bacteria in fasta format (one bacterium per file as well).

These can be downloaded from NCBI right away.

== Command ==

mpiexec -n 64 Ray \
-p 1_1.fastq -p 1_2.fastq \
-search NCBI-bacteria-directory \
-search NCBI-viruses-directory \
-o RayMicrobiomeAnalysis

== Input directories ==

NCBI-bacteria-directory/ecoli.fasta
NCBI-bacteria-directory/spneumo.fasta
...

NCBI-viruses-directory/phix.fasta
...


== Output ==

RayMicrobiomeAnalysis/ contains the usual files.

For a list of output files, see Ray -help

The new files produced by the -search option are:


RayMicrobiomeAnalysis/
	BiologicalAbundances/
		_DenovoAssembly/
			Contigs.tsv
			*.CoverageData.xml

		_Coloring/
		_Frequencies/

		NCBI-bacteria-directory/
			ContigIdentifications.tsv
			_Files.tsv
			SequenceAbundances.xml

		NCBI-viruses-directory/
			ContigIdentifications.tsv
			_Files.tsv
			SequenceAbundances.xml

Hello,

On 19/09/12 11:45 PM, Habib R wrote:
> From previous build version of Ray, I found 0.Profile.Bacteria.tsv under the
> BiologicalAbundances dir. 
> What is this? How can I related this file to the ContigIdentification.tsv
> and/or 
> SequenceAbundances.xml under Bacteria subdir?
> 

SequenceAbundances.xml contains the primary copy of information for your
profiled sample. There are XSL files in ray/scripts/xsl-xml/ to convert the XML file to
tabular format, albeit with less information in it though.


With -search, Ray colors the graph after the de novo assembly to assign "what
is where".

For each contig path in your graph (that is, in your assembly), Ray counts the
number
of matches in the contig path.

So a line in ContigIdentification.tsv tells you that a given contig has N
"Matches in contig" for a given reference sequence, and that the matches cover "Contig length
ratio" of the contig, and "Sequence length ratio"


== Note ==

The virtual processor and communicator are heavily utilised here.
