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History



File Date Author Commit
AmosCmp16Spipeline 2010-03-19 bhaas [r171] update
ChimeraSlayer 2011-05-19 bhaas [r222] update
NAST-iEr 2011-05-19 bhaas [r220] update
RESOURCES 2010-04-24 bhaas [r193] add
TreeChopper 2010-11-01 bhaas [r206] update
WigeoN 2010-11-01 bhaas [r207] update
__deprecated_BlastAssistedAssembler 2010-02-14 bhaas [r163] update, including deprecating software no longe...
__deprecated_bioname 2010-02-14 bhaas [r163] update, including deprecating software no longe...
docs 2011-05-19 bhaas [r221] update
Makefile 2010-04-24 bhaas [r191] renamed CSlayer utilities
README 2010-04-29 bhaas [r195] update

Read Me

Contents:

The microbiomeutil/ package comes with the following:

	ChimeraSlayer/  ChimeraSlayer for chimera detection.

	NAST-iEr/  NAST-based alignment tool.

	WigeoN/    A reimplementation of the Pintail 16S anomaly detection utility 

	RESOURCES/  Reference 16S sequences and NAST-alignments that the tools above leverage.




Installation Requirements:

	The following software tools must be separately installed and made available via your standard PATH setting.

	       megablast:  http://www.ncbi.nlm.nih.gov/BLAST/download.shtml

           cdbtools:  http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/download.pl?ftp_dir=software&file_dir=cdbfasta/cdbfasta.
tar.gz




Building and Testing:

In the microbiomeutil/ directory, type:

     make 

The above will build the NAST-iEr alignment utility which is written in C.  The other tools are all written in Perl and so don't need to be compiled.


Run tests in the following order:

	make testNast

	make testChimeraSlayer

	make testWigeon


    (or just type:  'make test' and it will cycle through each separately)


Documentation for using the various tools is included on the microbiomeutil website:  http://microbiomeutil.sf.net


Questions, comments, etc?  Please contact Brian Haas via bhaas@broadinstitute.org