Main Content


Retrieve table with object properties and equivalent Bowtie 2 options



tbl = getBowtie2Table(object) returns a table with all the object properties and corresponding Bowtie 2 options [1].

getBowtie2Table requires the Bioinformatics Toolbox™ Interface for Bowtie Aligner. If this support package is not installed, then the function provides a download link. For details, see Bioinformatics Toolbox Software Support Packages.


getBowtie2Table is supported on Mac and UNIX® platforms only.


collapse all

Create a Bowtie2AlignOptions object.

 alignOpt = Bowtie2AlignOptions;

Retrieve the equivalent Bowtie 2 options for all the object properties.

ans =

  47×2 table

         PropertyName           Bowtie2OptionName  
    ______________________    _____________________

    'AllowDovetail'           '--dovetail'         
    'AmbiguousPenalty'        '--np'               
    'Encoding_Phred33'        '--phred33'          
    'Encoding_Phred64'        '--phred64'          
    'Encoding_Solexa'         '--solexa-quals'     
    'ExcludeContain'          '--no-contain'       
    'ExcludeDiscordant'       '--no-discordant'    
    'ExcludeMixed'            '--no-mixed'         
    'ExcludeOverlap'          '--no-overlap'       
    'ExcludeUnaligned'        '--no-unal'          
    'IgnoreQuality'           '--ignore-quals'     
    'MatchBonus'              '--ma'               
    'MaxAmbiguousFunction'    '--n-ceil'           
    'MemoryMappedIndex'       '--mm'               
    'MinScoreFunction'        '--score-min'        
    'MismatchPenalty'         '--mp'               
    'Mode_EndToEnd'           '--end-to-end'       
    'Mode_Local'              '--local'            
    'NoGapPositions'          '--gbar'             
    'Nondeterministic'        '--non-deterministic'
    'NumAlignments'           '-k'                 
    'NumAlignments_All'       '-a'                 
    'NumAlignments_Best'      ''                   
    'NumReseedings'           '-R'                 
    'NumSeedExtensions'       '-D'                 
    'NumSeedMismatches'       '-N'                 
    'NumThreads'              '--threads'          
    'NumThreads'              '-p'                 
    'Offrate'                 '--offrate'          
    'Offrate'                 '-o'                 
    'PadPositions'            '--dpad'             
    'ReadGapCosts'            '--rdg'              
    'ReadGroup'               '--rg'               
    'ReadGroupID'             '--rg-id'            
    'RefGapCosts'             '--rfg'              
    'Reorder'                 '--reorder'          
    'Seed'                    '--seed'             
    'SeedIntervalFunction'    '-i'                 
    'SeedLength'              '-L'                 
    'Skip'                    '--skip'             
    'Skip'                    '-s'                 
    'Trim3'                   '--trim3'            
    'Trim3'                   '-3'                 
    'Trim5'                   '--trim5'            
    'Trim5'                   '-5'                 
    'UpTo'                    '--upto'             
    'UpTo'                    '-u'        

Input Arguments

collapse all

Bowtie 2 options object, specified as a Bowtie2AlignOptions, Bowtie2InspectOptions, or Bowtie2BuildOptions object.

Example: alignOpt

Output Arguments

collapse all

Object properties and the corresponding Bowtie2 options [1], returned as a table.


[1] Langmead, B., and S. Salzberg. "Fast gapped-read alignment with Bowtie 2." Nature Methods. 9, 2012, 357–359.

Introduced in R2018a