Christopher Fields
and 1 contributors


Bio::Tools::Run::BWA - Run wrapper for the BWA short-read assembler *BETA*


 # create an assembly

 # run BWA commands separately


This module provides a wrapper interface for Heng Li's reference-directed short read assembly suite bwa (see for manuals and downloads).

Manipulating the alignments requires samtools ( and Lincoln Stein's package Bio-SamTools (

There are two modes of action.

  • Easy assembly

    The first is a simple pipeline through the maq commands, taking your read data in and squirting out an assembly object of type Bio::Assembly::IO::maq. The pipeline is based on the one performed by easyrun:

     Action                  maq commands
     ------                  ------------
     data conversion to      fasta2bfa, fastq2bfq
     maq binary formats
     map sequence reads      map
     to reference seq
     assemble, creating      assemble
     convert map & cns       mapview, cns2fq
     files to plaintext
     (for B:A:IO:maq)

    Command-line options can be directed to the map, assemble, and cns2fq steps. See "OPTIONS" below.

  • BWA command mode

    The second mode is direct access to bwa commands. To run a bwa command, construct a run factory, specifying the desired command using the -command argument in the factory constructor, along with options specific to that command (see "OPTIONS"):

     $bwafac = Bio::Tools::Run::BWA->new( -command => 'fasta2bfa' );

    To execute, use the run_bwa methods. Input and output files are specified in the arguments of run_bwa (see "FILES"):

     $bwafac->run_bwa( -fas => "myref.fas", -bfa => "myref.bfa" );


bwa is complex, with many subprograms (commands) and command-line options and file specs for each. This module attempts to provide commands and options comprehensively. You can browse the choices like so:

 $bwafac = Bio::Tools::Run::BWA->new( -command => 'aln' );
 # all maq commands
 @all_commands = $bwafac->available_parameters('commands'); 
 @all_commands = $bwafac->available_commands; # alias
 # just for aln
 @aln_params = $bwafac->available_parameters('params');
 @aln_switches = $bwafac->available_parameters('switches');
 @aln_all_options = $bwafac->available_parameters();

Reasonably mnemonic names have been assigned to the single-letter command line options. These are the names returned by available_parameters, and can be used in the factory constructor like typical BioPerl named parameters.

See for the gory details.


When a command requires filenames, these are provided to the run_bwa method, not the constructor (new()). To see the set of files required by a command, use available_parameters('filespec') or the alias filespec():

  $bwafac = Bio::Tools::Run::BWA->new( -command => 'aln' );
  @filespec = $bwafac->filespec;

This example returns the following array:


This indicates that the FASTA database (faq) and the FASTQ reads (faq) MUST be specified, and the STDOUT of this program (SA coordinates) MAY be slurped into a file specified in the run_bwa argument list:

 $bwafac->run_bwa( -fas => 'my.db.fas', -faq => 'reads.faq',
                   -sai => 'out.sai' );

If files are not specified per the filespec, text sent to STDOUT and STDERR is saved and is accessible with $bwafac-stdout()> and $bwafac-stderr()>.


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

AUTHOR - Mark A. Jensen

 Email maj -at- fortinbras -dot- us


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $obj = new Bio::Tools::Run::BWA();
 Function: Builds a new Bio::Tools::Run::BWA object
 Returns : an instance of Bio::Tools::Run::BWA
 Args    :


 Title   : run
 Usage   : $assembly = $bwafac->run( @args );
 Function: Run the bwa assembly pipeline. 
 Returns : Assembly results (file, IO object or Assembly object)
 Args    : - fastq file containing single-end reads
           - fasta file containing the reference sequence
           - [optional] fastq file containing paired-end reads 


 Title   : run_bwa
 Usage   : $obj->run_bwa( @file_args )
 Function: Run a bwa command as specified during object contruction
 Returns : 
 Args    : a specification of the files to operate on:


 Title   : stdout
 Usage   : $fac->stdout()
 Function: store the output from STDOUT for the run, 
           if no file specified in run_maq()
 Example : 
 Returns : scalar string
 Args    : on set, new value (a scalar or undef, optional)


 Title   : stderr
 Usage   : $fac->stderr()
 Function: store the output from STDERR for the run, 
           if no file is specified in run_maq()
 Example : 
 Returns : scalar string
 Args    : on set, new value (a scalar or undef, optional)

Bio::Tools::Run::AssemblerBase overrides






 Convert input fastq and fasta to maq format.


 Title   : _collate_subcmd_args
 Usage   : $args_hash = $self->_collate_subcmd_args
 Function: collate parameters and switches into command-specific
           arg lists for passing to new()
 Returns : hash of named argument lists
 Args    : [optional] composite cmd prefix (scalar string) 
           [default is 'run']


 Title   :   _run
 Usage   :   $factory->_run()
 Function:   Run a bwa assembly pipeline
 Returns :   a text-formatted sam alignment
 Args    :   - single end read file in maq bfq format
             - reference seq file in maq bfa format
             - [optional] paired end read file in maq bfq format


 Title   : available_parameters
 Usage   : @cmds = $fac->available_commands('commands');
 Function: Use to browse available commands, params, or switches
 Returns : array of scalar strings
 Args    : 'commands' : all bwa commands
           'params'   : parameters for this object's command
           'switches' : boolean switches for this object's command
           'filespec' : the filename spec for this object's command
 4Geeks  : Overrides Bio::ParameterBaseI via