Magnet: an ultra-fast and high-sensitive tool to separate exogenous of endogenous DNA
Get Magnet and make the project, using:
git clone https://github.com/pratas/Magnet.git
cd Magnet
cmake .
makeNote, an already compiled version of Magnet is available for 64 bit Linux OS in
the bin/ directory.
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.
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 test2will be exactly the same as running
./Magnet -l 3 -t 0.5 -o out.fq test1.fa test2.fqIf you want to compare Magnet with other methods, set the parameters in
run.sh bash script, at scripts/ directory, then run it:
./run.shWith this script, you can download the datasets, install the tools, run these tools, and finally, print the results.
To see the possible options, type:
./cryfawhich 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],
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.
- Release 1.
Please let us know if there is any issues.
Magnet is under GPL v3 license. For more information, click here.