metAMOS configuration summary:
Time and Date:		2012-10-25
Working directory:	/fs/wrenhomes/sergek/metAMOS/Test/test_fcp
Prefix:			proba
K-Mer:			55
Threads:		8
Taxonomic level:	phylum
Verbose:		True
Steps to skip:		
Steps to force:		Preprocess

Step-specific configuration:
[abundance]
MetaPhyler
	/fs/wrenhomes/sergek/metAMOS/Utilities/cpp/Linux-x86_64
	Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.

[scaffold]
Bambus 2
	/fs/wrenhomes/sergek/metAMOS/AMOS/Linux-x86_64/bin
	Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 27(21): 2964-2971 2011.

[findorfs]
FragGeneScan
	/fs/wrenhomes/sergek/metAMOS/Utilities/cpp/Linux-x86_64
	Rho M, Tang H, Ye Y: FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Research 2010, 38:e191-e191.

[mapreads]
Bowtie
	/fs/wrenhomes/sergek/metAMOS/Utilities/cpp/Linux-x86_64
	Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Epub 2009 Mar 4.

[assemble]
SOAPdenovo
	/fs/wrenhomes/sergek/metAMOS/Utilities
	Li Y, Hu Y, Bolund L, Wang J: State of the art de novo assembly of human genomes from massively parallel sequencing data.Human genomics 2010, 4:271-277.

[classify]
FCP,Naive Bayesian Classifier
	/fs/wrenhomes/sergek/metAMOS/Utilities/cpp/Linux-x86_64
	Macdonald NJ, Parks DH, Beiko RG. Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Res. 2012 Apr 24.

[other]
Krona
	/fs/wrenhomes/sergek/metAMOS/KronaTools/bin
	Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30;12:385.