FOCUS2 Files

FOCUS2: Agile and sensitive classification of metagenomics data using a reduced database || version 0.1
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(c)            Silva, G. G. Z., B. E. Dutilh, and R. A. Edwards: 
		FOCUS2: Agile and sensitive classification of metagenomics data using a reduced database (unplublished).
website: 	https://edwards.sdsu.edu/FOCUS2
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Program: focus2__downloadDB.py.py: Downloads the FOCUS2 database
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(1) USAGE
python focus2__downloadDB.py

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Program: focus2.py: FOCUS2 main program
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(1) USAGE
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FOCUS2: agile and sensitive classification of metagenomics data using a reduced database
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Options:
         -h          ------: print help
         -q          string: folder with multiple FASTA/FASTQ files
         -dir        string: output directory
         -o          string: project name (default 'my_project')
         -mi         float:  minimum identity (default 60 %)
         -ml         int:    minimum alignment (default 45 nucleotides)
         -k          int:    k-mer frequency used on FOCUS (default: 7) (6/7)
         -n          int:    normalize counts minimum alignment (0:False/1:True)(default: 0)
         -t          int:    number of threads (default 1)
         -e          float:  e-value (default 0.00001)
         -a          string: aligner (blastn/hsblastn) (default: blastn)
         -s          int:    split profiling in different levels (0:False/1:True)(default: 1)
         -bootstrap  int:    resamples the data to have more confidence in the results (0:False/1:True)(default: 0)
         -ns         int:    number of resampling per sample (default: 10)
         -b          float:  % of sequences to resample (default: 80.0)
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example> python focus2.py -q input/ -dir output/
	 
(2) OUTPUT
FOCUS2 output will be add the folder selected in -dir

(4) DEPENDENCIES
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Python >= 2.6.X < 3.Y: http://www.python.org/download
Jellyfish: http://www.cbcb.umd.edu/software/jellyfish
Numpy: http://sourceforge.net/projects/numpy/files/NumPy
SciPy: http://sourceforge.net/projects/scipy

One of the below aligners:
BLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
HS-BLASTN: https://github.com/chenying2016/queries

COPYRIGHT AND LICENSE
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Copyright (C) 2015-2016  Genivaldo Gueiros Z. Silva

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.  See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with
this program.  If not, see <http://www.gnu.org/licenses/>.