joaorafaelalmeida/Magnet

Magnet: an ultra-fast and high-sensitive tool to separate exogenous of endogenous DNA

INSTALL

Get Magnet and make the project, using:

git clone https://github.com/pratas/Magnet.git
cd Magnet
cmake .
make

Note, an already compiled version of Magnet is available for 64 bit Linux OS in the bin/ directory.

RUN

If you want to run Magnet in stand-alone mode, use the following command:

./Magnet [OPTION]... [IN_FILE_1] [IN_FILE_2]

For example, to compact & encrypt:

./Magnet -l 3 -t 0.5 -o out.fq seq.fa in.fq

Options are described in the following sections.

Input file format

Magnet automatically detects a genomic data file format by looking inside the file and not by the file extension. For example, a FASTA file, say “test”, can be fed into Magnet as "test", "test.fa", "test.fasta", "test.fas", "test.fsa" or any other file extension. By this explanation, running

./Magnet -l 3 -t 0.5 -o out.fq test1 test2

will be exactly the same as running

./Magnet -l 3 -t 0.5 -o out.fq test1.fa test2.fq

Compare Magnet with other methods

If you want to compare Magnet with other methods, set the parameters in run.sh bash script, at scripts/ directory, then run it:

./run.sh

With this script, you can download the datasets, install the tools, run these tools, and finally, print the results.

OPTIONS

To see the possible options, type:

./cryfa

which provides the following:

NAME                                                                     
      Magnet v18.11 - an ultra-fast and high-sensitive tool              
                      to separate exogenous of endogenous DNA.           
                                                                         
AUTHORS                                                                  
      Diogo Pratas        pratas@ua.pt                                   
      Morteza Hosseini    seyedmorteza@ua.pt                             
      Armando J. Pinho    ap@ua.pt                                       
                                                                         
SYNOPSIS                                                                 
      ./Magnet [OPTION]... [IN_FILE_1] [IN_FILE_2]                       
                                                                         
SAMPLE                                                                   
      Filter exogenous: ./Magnet -l 3 -t 0.5 -o out.fq in.fa seq.fq      
                                                                         
DESCRIPTION                                                              
      Separate exogenous of endogenous DNA.                              
      Isolates specific reads with similarity to other sequence(s).      
      Filters FASTQ reads by similarity to FASTA genome sequence(s).     
      The genome sequence may be constituted by contigs, scaffolds,      
      or assembled sequences.                                            
                                                                         
      -h,  --help                                                        
           usage guide (help menu).                                      
                                                                         
      -F,  --force                                                       
           force mode. Overwrites old files.                             
                                                                         
      -v,  --verbose                                                     
           verbose mode (more information).                              
                                                                         
      -V,  --version                                                     
           Display version number, license and basic information.        

      -i,  --invert
           Inverts search. Filters only the complement.

      -s,  --show                                                        
           Show similarity levels [1;44].                               
                                                                         
      -l [NUMBER],  --level [NUMBER]                                     
           Similarity level (integer).                                   
           Default level: 1.                                            
           It defines sensitivity in balance with computational          
           resources (RAM & time). Use -s for levels perception.         
                                                                         
      -t [NUMBER],  --threshold [NUMBER]                                 
           Threshold of similarity (real).                               
           Value contained in [0.0;1.0].                                 
                                                                         
      -p [NUMBER],  --portion [NUMBER]                                   
           Portion of acceptance.                                        
           Acceptance bases (default: 2).                               
                                                                         
      -o [OUT_FILE],  --output [OUT_FILE]                                
           Output file name.                                             
           The OUT_FILE will contain the filtered reads.                 
                                                                         
      -n [NUMBER],  --threads [NUMBER]                                   
           Number of threads.                                            
                                                                         
      [IN_FILE_1]                                                        
           Input FASTA file name -- MANDATORY.                           
                                                                         
      [IN_FILE_2]                                                        
           Input FASTQ file name -- MANDATORY.                           
                                                                         
COPYRIGHT                                                                
    Copyright (C) 2014-2018, IEETA, University of Aveiro.                
    This is a Free software, under GPLv3. You may redistribute           
    copies of it under the terms of the GNU - General Public             
    License v3 <http://www.gnu.org/licenses/gpl.html>. There             
    is NOT ANY WARRANTY, to the extent permitted by law.

Magnet uses standard ouput stream, hence, its output can be directly integrated with pipelines.

If you are interested in the topic of "metagenomics" and "ancient DNA", you can read the articles [1], [2],

CITE

Please cite the followings, if you use Magnet:

D. Pratas, M. Hosseini and A.J. Pinho, "Magnet: an ultra-fast and high-sensitive tool to separate exogenous of endogenous DNA," ?, 2018.

RELEASES

Release 1.

ISSUES

Please let us know if there is any issues.

LICENSE

Magnet is under GPL v3 license. For more information, click here.

joaorafaelalmeida / Magnet