NAME

         Bio::Tools::Run::Minimo - Wrapper for local execution of the Minimo assembler

SYNOPSIS

         use Bio::Tools::Run::Minimo;
         # Run Minmo using an input FASTA file
         my $factory = Bio::Tools::Run::Minimo->new( -minimum_overlap_length => 35 );
         my $asm_obj = $factory->run($fasta_file, $qual_file);
         # An assembly object is returned by default
         for my $contig ($assembly->all_contigs) {
           ... do something ...
         }

         # Read some sequences
         use Bio::SeqIO;
         my $sio = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta');
         my @seqs;
         while (my $seq = $sio->next_seq()) {
           push @seqs,$seq;
         }

         # Run Minimo using input sequence objects and returning an assembly file
         my $asm_file = 'results.ace';
         $factory->out_type($asm_file);
         $factory->run(\@seqs);

DESCRIPTION

         Wrapper module for the local execution of the DNA assembly program Minimo.
         Minimo is based on AMOS (http://sourceforge.net/apps/mediawiki/amos/) and
         implements the same conservative assembly algorithm as Minimus
         (http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus).

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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

       bioperl-l@bioperl.org

       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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Florent E Angly

        Email: florent-dot-angly-at-gmail-dot-com

APPENDIX

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

   new
        Title   : new
        Usage   : $assembler->new( -min_len   => 50,
                                   -min_ident => 95 );
        Function: Creates a Minimo factory
        Returns : A Bio::Tools::Run::Minimo object
        Args    : Minimo options available in this module:
            qual_in      Input quality score file
            good_qual    Quality score to set for bases within the clear
                           range if no quality file was given (default: 30)
            bad_qual     Quality score to set for bases outside clear range
                           if no quality file was given (default: 10). If your
                           sequences are trimmed, try the same value as GOOD_QUAL.
            min_len / minimum_overlap_length
                         Minimum contig overlap length (between 20 and 100 bp,
                           default: 35)
            min_ident / minimum_overlap_similarity
                         Minimum contig overlap identity percentage (between 0
                           and 100 %, default: 98)
            aln_wiggle   Alignment wiggle value when determining the consensus
                           sequence (default: 2 bp)
            out_prefix   Prefix to use for the output file path and name

   out_type
        Title   : out_type
        Usage   : $factory->out_type('Bio::Assembly::ScaffoldI')
        Function: Get/set the desired type of output
        Returns : The type of results to return
        Args    : Desired type of results to return (optional):
                        'Bio::Assembly::IO' object
                        'Bio::Assembly::ScaffoldI' object (default)
                        The name of a file to save the results in

   run
        Title   :   run
        Usage   :   $factory->run($fasta_file);
        Function:   Run TIGR Assembler
        Returns :   - a Bio::Assembly::ScaffoldI object, a Bio::Assembly::IO
                      object, a filename, or undef if all sequences were too small to
                      be usable
        Returns :   Assembly results (file, IO object or assembly object)
        Args    :   - sequence input (FASTA file or sequence object arrayref)
                    - optional quality score input (QUAL file or quality score object
                      arrayref)

   _run
        Title   :   _run
        Usage   :   $factory->_run()
        Function:   Make a system call and run TIGR Assembler
        Returns :   An assembly file
        Args    :   - FASTA file
                    - optional QUAL file

   _clean_file
        Title   :   _clean_file
        Usage   :   $factory->_clean_file($file)
        Function:   Clean file in place by removing NULL characters. NULL characters
                    can be present in the output files of AMOS 2.0.8 but they do not
                    validate as proper sequence characters in Bioperl.
        Returns :   1 for success
        Args    :   Filename