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Alignment-free simulation, computation, and visualization of Low-compexity regions in biological data

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Conda License: GPL v3 Speed NoFP NoFP AFM

AlcoR

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.

INSTALLATION

Conda

Install Miniconda, then run the following:

conda install -y -c bioconda alcor

Otherwise, 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

EXECUTION

Run AlcoR

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

PARAMETERS

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 

CITATION

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

ISSUES

For any issue let us know at issues link.

LICENSE

GPL v3.

For more information:

http://www.gnu.org/licenses/gpl-3.0.html