https://cobilab.github.io/alcor
Alignment-free simulation, mapping, and visualization of low-complexity regions in FASTA data.
AlcoR provides the ability of fast sequence characterization through low-complexity regions, ideally for scenarios entangling the presence of new or unknown sequences. AlcoR offers important analysis advantages, such as the high-sensitivity, speed, and does not provide false positives, ideally to be applied in the current Telomere-to-telomere (T2T) sequencing and assembly methodologies. AlcoR is implemented in C language using multi-threading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence in FASTA format.
The AlcoR tool contains one main menu (command: AlcoR) with the five sub menus for computing the features that it provides, namely
- info: it provides information of the length and GC percentage for each FASTA read;
- extract: extracts a sequence of a FASTA file using positional coordinates (independent from the existing headers of the FASTA files);
- mapper: computes the low-complexity regions of a FASTA read while providing bidirectional complexity profiles and further structural similarity analysis;
- simulation: FASTA sequence simulation with features: file extraction, random generation, sequence modeling. Additionally, it allwos to apply specific SNPs probability mutations;
- visual: computes an SVG file with the respective map containing the low-complexity regions.
Install Miniconda, then run the following:
conda install -y -c bioconda alcorOtherwise, CMake is needed for installation (http://www.cmake.org/). You can download it directly from http://www.cmake.org/cmake/resources/software.html or use an appropriate packet manager. In the following instructions we show the procedure to install, compile and run AlcoR:
sudo apt-get install cmake git git clone https://github.com/cobilab/alcor.git cd alcor/src/ cmake . make
Run AlcoR FASTA simulation tool:
AlcoR simulation -rs 2000:0:1:0:0:0 -rs 2000:0:11:0:0:0 -rs 2000:0:1:0:0:0 -rs 2000:0:71:0:0:0 > sample.fasta;
Run AlcoR low-complexity mapper:
AlcoR mapper -v -n -m 13:50:0:1:10:0.9/5:10:0.9 --dna -w 3 -t 0.5 sample.fasta
To see the possible options type
AlcoR
or
AlcoR -h
If you are not interested in viewing each sub-program option, type
AlcoR info -h AlcoR extract -h AlcoR mapper -h AlcoR simulation -h AlcoR visual -h
The info menu contains the following information
NAME
AlcoR info
DESCRIPTION
It provides length and GC information of each FASTA read.
PARAMETERS
-h, --help
usage guide (help menu),
-v, --verbose
verbose mode (more information),
-m [INT], --header-max [INT]
maximum header size for exporting information,
[FILE]
input sequence filename (to analyze) -- MANDATORY,
FASTA file to retrieve information (last argument).
SYNOPSIS
AlcoR info [OPTION]... [FILE]
EXAMPLE
AlcoR info -v -f seq.fa
The extract menu contains the following information
NAME
AlcoR extract
DESCRIPTION
Extracts a sequence from a FASTA file using coordinates.
PARAMETERS
-h, --help
usage guide (help menu),
-v, --verbose
verbose mode (more information),
-f, --fasta
outputs a FASTA format with the sequence,
-i [INT], --init [INT]
initial position for extracting the sequence,
-e [INT], --end [INT]
end position for extracting the sequence,
[FILE]
input sequence filename (to analyze) -- MANDATORY,
FASTA file for the extraction (last argument).
SYNOPSIS
AlcoR extract [OPTION]... [FILE]
EXAMPLE
AlcoR extract -v -f -i 101 -e 301 seq.fa
The mapper menu contains the following information
NAME
AlcoR mapper
DESCRIPTION
Computes the low-complexity regions of a sequence (FASTA).
PARAMETERS
-h, --help
usage guide (help menu),
-v, --verbose
verbose mode (more information),
-n, --no-size
does not print the segmented map with the header size,
-e, --hide
it hides (deletes) the final smooth profile,
-d, --dna
considers exclusively DNA alphabet {A,C,G,T},
it also provides inverted repeats models,
flag absence considers inversions (without complements),
-c [INT], --color [INT]
Color Hue to be used in visualization,
-t [FLOAT], --threshold [FLOAT]
threshold to segment regions (real),
-w [INT], --window [INT]
window size to smooth the minimum of both directions
of compression using a moving average filter (int),
-i [INT], --ignore [INT]
ignore lengths of segmented regions below this value,
-k, --mask
it masks a FASTA sequence (LCRs appear in lower case),
-o, --output-mask
output FASTA filename with the masked sequence,
-r, --renormalize
renormalize the positions of a multi-FASTA file,
-f [STRING], --prefix [STRING]
use this prefix for the output of renormalize (if on),
-p, --show-parameters
show parameters of the models for optimization,
-s, --show-levels
show pre-computed compression levels (parameters),
-l [INT], --level [INT]
compression level (integer),
it defines compressibility in balance with computational
resources (RAM and time), use -s for levels perception,
[FILE]
input sequence filename (to analyze) -- MANDATORY,
FASTA file for the analysis (last argument).
SYNOPSIS
AlcoR mapper [OPTION]... [FILE]
EXAMPLE
AlcoR mapper -v -w 10 -m 13:50:0:1:10:0.9/5:10:0.9 -k -o m.fa seq.fa
The simulation menu contains the following information
NAME
AlcoR simulation
DESCRIPTION
Simulation of FASTA sequences with specific features.
PARAMETERS
-h, --help
usage guide (help menu),
-v, --verbose
verbose mode (more information),
-n, --no-dna
Does not consider a DNA alphabet {A,C,G,T},
it provides possible inversions without complements,
-a [STRING], --alphabet [STRING]
alphabet to consider (Default: ACGT),
-fs [FEATURES], --file-segment [FEATURES]
FASTA file segment features:
| [init:end:ir:seed:subs:adds:dels:file]
| ...
init [INT] - initial position of the segment,
end [INT] - ending position of the segment,
ir [INT] - segment inverted if 1, otherwise 0,
seed [INT] - initial number for random generation,
subs [FLOAT] - probability of substitution mutation,
adds [FLOAT] - probability of addition mutation,
dels [FLOAT] - probability of deletion mutation,
file [FILE] - FASTA filename for extracting segment,
-rs [FEATURES], --rand-segment [FEATURES]
Random segment features:
| [size:ir:seed:subs:adds:dels]
| ...
size [INT] - length of the segment,
ir [INT] - segment inverted if 1, otherwise 0,
seed [INT] - initial number for random generation,
subs [FLOAT] - probability of substitution mutation,
adds [FLOAT] - probability of addition mutation,
dels [FLOAT] - probability of deletion mutation,
-ms [FEATURES], --model-segment [FEATURES]
Model segment features:
| [size:ctx:bet:ir:seed:subs:adds:dels:file]
| ...
size [INT] - length of the segment,
ctx [INT] - context to model and simulate,
bet [INT] - intensity for higher bet strength,
ir [INT] - segment inverted if 1, otherwise 0,
seed [INT] - initial number for random generation,
subs [FLOAT] - probability of substitution mutation,
adds [FLOAT] - probability of addition mutation,
dels [FLOAT] - probability of deletion mutation,
file [FILE] - FASTA filename for learning model,
SYNOPSIS
AlcoR simulation [OPTION]... > output.fa
EXAMPLE
AlcoR simulation -rs 50:0:1:0.1:0:0 -ms 80:7:50:0:7:0:0:0:x.fa
The visual menu contains the following information
NAME
AlcoR visual
DESCRIPTION
Creates an SVG map with the identified regions.
PARAMETERS
-h, --help
usage guide (help menu),
-v, --verbose
verbose mode (more information),
-w [INT], --width [INT]
horizontal width (thickness) of each bar,
-s [INT], --space [INT]
space between each bar,
-e [INT], --enlarge [INT]
enlargement of each region (increase visibility),
-c, --strict-corner
it paints each bar with strict corners (NO round),
-b [STRING], --back-color [STRING]
background color in RGB format (example: FFFFFF),
-a [STRING], --border-color [STRING]
bar border color in RGB format (example: 000000),
-o [FILE], --output [FILE]
filename of the SVG output map,
[FILE]:[FILE]:...
input position filenames (to analyze) -- MANDATORY,
multiple files can be used with : split token.
SYNOPSIS
AlcoR visual [OPTION]... [FILE]:...
EXAMPLE
AlcoR visual -v -o map.svg pos1.txt:pos2.txt:pos3.txt
On using this software/method please cite:
- J. M. Silva, W. Qi, A. J. Pinho, D. Pratas, AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data, GigaScience, Volume 12, 2023. Download
For any issue let us know at issues link.
GPL v3.
For more information:
http://www.gnu.org/licenses/gpl-3.0.html