#FOCUS2 Agile and sensitive classification of metagenomics data using a reduced database || version 0.1
(c) Genivaldo G. Z. Silva, Daniel A. Cuevas, J. Matthew Haggerty, Michael Doane, Elizabeth A. Dinsdale, Bas E. Dutilh, and Robert A. Edwards. Ecological Implications of Metagenomics Data Analysis (unplublished).
website: https://edwards.sdsu.edu/FOCUS2
Program
focus2__downloadDB.py: Downloads the FOCUS2 database
(1) USAGE python focus2__downloadDB.py
Program
focus2.py: FOCUS2 main program
(1) USAGE
Options:
-h none
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: hsblastn)
-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)
example> python focus2.py -q input/ -dir output/
(2) OUTPUT FOCUS2 output will be add the folder selected in -dir
Program
(1) FOCUS2(R)
Options:
-h none
print help
-q string
folder with multiple FASTA/FASTQ files
-b file
binning file for '-q' from FOCUS2
-dir string
output directory
-mi float
minimum identity (default 60 %)
-ml int
minimum alignment (default 45 nucleotides)
-e float
e-value (default 0.00001)
-t int
number of threads (default 1)
-o string
project name (default 'my_project')
example> python focus2r.py -q FASTA/FASTQ -b focus2_binning -dir output/
(2) OUTPUT FOCUS2R output will be add the folder selected in -dir
(3) OBSERVATION
- FOCUS2(R) only uses hs-blastn as aligner
DEPENDENCIES
- 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
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/.