This is a collection of easy-to-use programs.

They all use the DarkFishTechnology. This technology enables:

 - Creating and purging cache entries that keeps the structure around
 - parallel processing
 - command logging
 - and more

BlueTsunami
	aligns reads to a reference with 'bwa bwasw' and generate a list of variations.

RedWave 
	aligns reads to a reference with 'bwa aln' and generate a list of variations.

OrangeSpark
	aligns reads to a reference with 'bowtie2' and generate a list of variations.

VioletRay
	performs a paired de novo assembly with Ray.

WhiteRay
	performs a paired de novo assembly for ChIP-Seq data with Ray.
	
GreenRay
	performs a paired de novo assembly, compute biological abundances in the de Bruijn graph,
	and identifies contigs based on provided libraries. With Ray.

== General architecture ==

=== RedWave, BlueTsunami and OrangeSpark ===

Data is stored in ApplicationCache.
Computation groups are purged when needed.

== RedWave ==

RedWave uses bash, coreutils, bwa, gzip, samstat, samtools and bcftools.


Usage:

	RedWave ReferenceSequence SampleDirectory NumberOfProcessors OutputDirectory


Example:

	RedWave reference.fasta Sample_test 8 Sample_test.analysis


== VioletRay ==

VioletRay utilises Open-MPI and Ray.

	VioletRay KmerLength SampleDirectory NumberOfProcessors OutputDirectory


Example:

	VioletRay 31 Sample_test 32 Sample_test.analysis