NAME

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

SYNOPSIS

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';
$factory->out_type($asm_file);
$factory->run(\@seqs);

DESCRIPTION

Wrapper module for the local execution of the proprietary DNA assembly
program GS De Novo Assembler (Newbler) from Roche/454 v2.0.00.20:
  http://www.454.com/products-solutions/analysis-tools/gs-de-novo-assembler.asp

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 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:
                       off).
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).

_check_sequence_input

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

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 can be:
              * a sequence object arrayref
              * a FASTA file
              * a SFF file and optional MID information. Example:
                  mid2@/home/xxx/myreads.sff
              * 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.

_run

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

cpanm Bio::DB::ESoap

perl -MCPAN -e shell
install Bio::DB::ESoap