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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
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 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