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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
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