Provided by: libbio-perl-run-perl_1.6.9-2_all bug


         Bio::Tools::Run::Newbler - Wrapper for local execution of Newbler


         use Bio::Tools::Run::Newbler;
         # Run Minmo using an input FASTA file
         my $factory = Bio::Tools::Run::Newbler->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 Newbler using input sequence objects and returning an assembly file
         my $asm_file = 'results.ace';


         Wrapper module for the local execution of the proprietary DNA assembly
         program GS De Novo Assembler (Newbler) from Roche/454 v2.0.00.20:


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AUTHOR - Florent E Angly

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


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

        Title   : new
        Usage   : $assembler->new( -min_len   => 50,
                                   -min_ident => 95 );
        Function: Creates a Newbler factory
        Returns : A Bio::Tools::Run::Newbler object
        Args    : Newbler options available in this module (from the Newbler manual):

        large                Shortcut some of the computationally expensive algorithms
                               to save some time. Useful for large or complex datasets
                               (default: off).
        ace_raw              Output the full "raw" read sequence (default: off).
        ace_trimmed          Output only the "trimmed" sequences (after low quality,
                               vector and key trimming) (default: on).
        expected_depth       Expected depth of the assembly. Filters out random-chance
                               level events at bigger depths. 0 means to not use the
                               expected depth information (default: 0).
        mid_conf_file        MID configuration file for decoding the multiplex data.
        no_trim              Disable the quality and primer trimming of the input
                               sequences (default: off).
        vector_trim          Specify a vector trimming database (in FASTA format) to
                               trim the ends of input sequences.
        vector_screen        Specify a vector screening database (in FASTA format) to
                               remove contaminants, i.e. input reads that align
                               against a sequence in the database.
        aln_identity_score   Set the alignment identity score. When multiple alignments
                               are found, it is the per-overlap column identity score
                               used to sort the overlaps for use in the progressive
                               alignment (default: 2).
        aln_difference_score Set the alignment difference score. For multiple alignments
                               this is the per-overlap difference score used to sort the
                               overlaps for use in the progressive multi-alignment
                               (default: -3).
        in_memory            Keep all sequence data in memory throughout the computation.
                               Can speed up the computation but requires more computer
                               memory (default: off).
        min_ovl_identity / minimum_overlap_similarity
                             Minimum overlap identity, i.e. the minimum percent identity
                               of overlaps used by the assembler (default: 40).
        min_ovl_length / minimum_overlap_length
                             Minimum overlap length, i.e. the minimum length of overlaps
                               considered by the assembler (default: 90). Warning: It
                               seems like this parameter is not respected by the program
                               in the current version
        no_auto_rescore      Do not use the quality score re-scoring algorithm (default:
        seed_count           Set the seed count parameter, the number of seeds required
                               in a window before an extension is made (default: 1).
        seed_length          Set the seed length parameter, i.e. the number of bases
                               between seed generation locations used in the exact
                               k-mer matching part of the overlap detection (between 6
                               16) (default: 16).
        seed_step            Set the seed step parameter, i.e. the number of bases used
                               for each seed in the exact k-mer matching part of the
                               overlap detection (i.e. the "k" value) (default: 12).
        no_duplicates        Treat each read as a separate read and do not group them
                               into duplicates for assembly or consensus calling
                              (default: off).

        Title   : _check_sequence_input
        Usage   : $assembler->_check_sequence_input($seqs)
        Function: Check that the sequence input is arrayref of sequence objects or
                  a FASTA file, or a MIDinfo + dir, or a MIDinfo + file. If not, an
                  error is thrown.
        Returns : 1 if the check passed
        Args    : sequence input

        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

        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 can be:
                      * a sequence object arrayref
                      * a FASTA file
                      * a SFF file and optional MID information. Example:
                      * the path to an run analysis directory and MID information
                    The reads must be between 50 and 2000 bp. Newbler does not support
                      for input quality files. See the Newbler manual for details.

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