NAME
Bio::Tools::Run::TigrAssembler - Wrapper for local execution of TIGR Assembler v2.0
SYNOPSIS
use Bio::Tools::Run::TigrAssembler;
my $assembler = Bio::Tools::Run::TigrAssembler->new();
# Pass the factory a Bio::Seq object array reference
# Returns a Bio::Assembly::Scaffold object array reference
my $asms = $assembler->run(\@seqs);
for my $asm (@$asms) {
# do something with assembled sequences
}DESCRIPTION
Wrapper module for the local execution of the DNA assembly program TIGR
Assembler v2.0. TIGR.
Assembler is open source software under The Artistic License and available at:
http://www.tigr.org/software/assembler/
The description enables to runs TIGR Assembler by feeding it sequence objects
and returning assembly objects. The input could be an array of Bio::PrimarySeq
or maybe Bio::Seq::Quality, in which case, the quality scores will
automatically be used during assembly. Sequences less than 40 bp long are
filtered out since they are not supported by TIGR Assembler. The
amount of memory in your machine may prevent you to assemble large sequence
datasets, but this module offers a way to split your dataset in smaller
datasets to be assembled _independently_. An array of Bio::Assembly::Scaffold
objects is returned.
If provided in the following way, TIGR Assembler will use additional
information present in the sequence descriptions for assembly:
>seq_name minimum_clone_length maximum_clone_length median_clone_length
clear_end5 clear_end3
or
>db|seq_name minimum_clone_length maximum_clone_length median_clone_length
clear_end5 clear_end3
e.g.
>GHIBF57F 500 3000 1750 33 587FEEDBACK
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 listsSupport
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://bugzilla.open-bio.org/AUTHOR - Florent E Angly
Email: florent-dot-angly-at-gmail-dot-comAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
program_name
Title : program_name
Usage : $assembler>program_name()
Function: get/set the program name
Returns: string
Args : stringprogram_dir
Title : program_dir
Usage : $assembler->program_dir()
Function: get/set the program dir
Returns: string
Args : stringmax_nof_seqs
Title : max_nof_seqs
Usage : $assembler->max_nof_seqs()
Function: get/set the maximum number number of sequences to assemble at once
Returns: string
Args : stringnew
Title : new
Usage : $assembler->new( -minimum_percent => 95,
-minimum_length => 50,
-include_singlets => 1);
Function: Creates a TIGR Assembler factory
Returns : Bio::Tools::Run::TigrAssembler object
Args : TIGR Assembler options available in this module:
minimum_percent: the minimum percent identity that two DNA fragments must
achieve over their entire region of overlap in order to be considered as a
possible assembly. Adjustments are made by the program to take into account
that the ends of sequences are lower quality and doubled base calls are the
most frequent sequencing error.
minimum_length: the minimum length two DNA fragments must overlap to be
considered as a possible assembly.
include_singlets: a flag which indicates that singletons (assemblies made up
of a single DNA fragment) should be included in the lassie output_file - the
default is to not include singletons.
max_err_32: the maximum number + 1 of alignment errors (mismatches or gaps)
allowed within any contiguous 32 base pairs in the overlap region between
two DNA fragments in the same assembly. This is meant to split apart splice
variants which have short splice differences and would not be disqualified
by the -p minimum_percent parameter.
consider_low_scores: a flag which causes even very LOW pairwise scores to be
considered - caution using this flag may cause longer run time and a worse
assembly.
maximum_end: the maximum length at the end of a DNA fragment that does not
match another overlapping DNA fragment (sometimes referred to as overhang)
that will not disqualify a DNA fragment from becoming part of an assembly.
ignore_tandem_32mers: a flag which causes tandem 32mers (a tandem 32mer is a
32mer which occurs more than once in at least one sequence read) to be
ignored (this is now the default behavior and this flag is for backward
compatability)
use_tandem_32mers: a flag which causes tandem 32mers to be used for pairwise
comparison opposite of the -t flag which is now the default).
safe_merging_stop: a flag which causes merging to stop when only sequences
which appear to be repeats are left and these cannot be merged based on
clone length constraints. not_random: a flag which indicates the DNA
fragments in the input_file should not be treated as random genomic
fragments for the purpose of determining repeat regions.
resort_after: specifies how many sequences should be merged before resorting
the possible merges based on clone constraints.run
Title : run
Usage : $obj->run(\@seqs, \@quals);
Function: Runs TIGR Assembler
Returns : a Bio::Assembly::ScaffoldI object array reference, or undef if all
sequences were too small to be usable
Args : - sequences as a Bio::PrimarySeqI or Bio::SeqI arrayref (e.g. can
be Bio::Seq::Quality for sequences and quality scores in a same
object)
- optional Bio::Seq::PrimaryQual arrayref of quality scores if
you have your scores in different objects from your sequences.
Must have same ID as sequences and same order_write_seq_file
Title : _write_seq_file
Usage : $assembler->_write_seq_file(\@seqs, \@quals)
Function: Write temporary FASTA and QUAL files on disk
Returns : name of FASTA file
name of QUAL file (undef if no quality scoress)
Args : Bio::PrimarySeq object array reference
optional quality objects array reference_run
Title : _run
Usage : $assembler->_run()
Function: Assembly step
Returns : Bio::Assembly::Scaffold object
assembly file location
Args : FASTA file location
QUAL file location [optional]