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Bio::Assembly::Tools::UseriContributed)Bio::Assembly::Tools::ContigSpectrum(3)

NAME
       Bio::Assembly::Tools::ContigSpectrum - create and manipulate contig
       spectra

SYNOPSIS
	 # Simple contig spectrum creation
	 my $csp1 = Bio::Assembly::Tools::ContigSpectrum->new(
	   -id	     =>	'csp1',
	   -spectrum =>	{ 1 => 10,
			  2 => 2,
			  3 => 1 } );

	 # ...or another way to	create a simple	contig spectrum
	 my $csp2 = Bio::Assembly::Tools::ContigSpectrum->new;
	 $csp2->id('csp2');
	 $csp2->spectrum({ 1 =>	20, 2 => 1, 4 => 1 });

	 # Get some information
	 print "This is	contig spectrum	".$csp->id."\n";
	 print "It contains ".$csp->nof_seq." sequences\n";
	 print "The largest contig has ".$csp->max_size." sequences\n";
	 print "The spectrum is: ".$csp->to_string($csp->spectrum)."\n";

	 # Let's add the contig	spectra
	 my $summed_csp	= Bio::Assembly::Tools::ContigSpectrum->new;
	 $summed_csp->add($csp1);
	 $summed_csp->add($csp2);
	 print "The summed contig spectrum is ".$summed_csp->to_string."\n";

	 # Make	an average
	 my $avg_csp = Bio::Assembly::Tools::ContigSpectrum->new;
	 $avg_csp = $avg_csp->average([$csp1, $csp2]);
	 print "The average contig spectrum is ".$avg_csp->to_string."\n";

	 # Get a contig	spectrum from an assembly
	 my $from_assembly = Bio::Assembly::Tools::ContigSpectrum->new(
	   -assembly	   => $assembly_object,
	   -eff_asm_params => 1);
	 print "The contig spectrum from assembly is ".$from_assembly->to_string."\n";

	 # Report advanced information (possible because eff_asm_params	= 1)
	 print "Average	sequence length: ".$from_assembly->avg_seq_len." bp\n";
	 print "Minimum	overlap	length:	".$from_assembly->min_overlap."	bp\n";
	 print "Average	overlap	length:	".$from_assembly->avg_overlap."	bp\n";
	 print "Minimum	overlap	match: ".$from_assembly->min_identity."	%\n";
	 print "Average	overlap	match: ".$from_assembly->avg_identity."	%\n";

	 # Assuming the	assembly object	contains sequences from	several	different
	 # metagenomes,	we have	a mixed	contig spectrum	from which a cross contig
	 # spectrum and	dissolved contig spectra can be	obtained
	 my $mixed_csp = $from_assembly;

	 # Calculate a dissolved contig	spectrum
	 my $meta1_dissolved = Bio::Assembly::Tools::ContigSpectrum->new(
	   -dissolve =>	[$mixed_csp, 'metagenome1'] );
	 my $meta2_dissolved = Bio::Assembly::Tools::ContigSpectrum->new(
	   -dissolve =>	[$mixed_csp, 'metagenome2'] );
	 print "The dissolved contig spectra are:\n".
	   $meta1_dissolved->to_string."\n".
	   $meta2_dissolved->to_string."\n";

	 # Determine a cross contig spectrum
	 my $cross_csp = Bio::Assembly::Tools::ContigSpectrum->new(
	   -cross => $mixed_csp	);
	 print "The cross contig spectrum is ".$cross_csp->to_string."\n";

	 # Score a contig spectrum (the	more abundant the contigs and the larger their
	 # size, the larger the	score)
	 my $csp_score = $csp->score( $csp->nof_seq );

DESCRIPTION
       The Bio::Assembly::Tools::ContigSpectrum	Perl module enables to
       manually	create contig spectra, import them from	assemblies, manipulate
       them, transform between different types of contig spectra and output
       them.

       Bio::Assembly::Tools::ContigSpectrum is a module	to create, manipulate
       and output contig spectra, assembly-derived data	used in	metagenomics
       (community genomics) for	diversity estimation.

   Background
       A contig	spectrum is the	count of the number of contigs of different
       size in an assembly. For	example, the contig spectrum [100 5 1 0	0 ...]
       means that there	were 100 singlets (1-contigs), 5 contigs of 2
       sequences (2-contigs), 1	contig of 3 sequences (3-contig) and no	larger
       contigs.

       An assembly can be produced from	a mixture of sequences from different
       metagenomes. The	contig obtained	from this assembly is a	mixed contig
       spectrum. The contribution of each metagenome in	this mixed contig
       spectrum	can be obtained	by determining a dissolved contig spectrum.

       Finally,	based on a mixed contig	spectrum, a cross contig spectrum can
       be determined. In a cross contig	spectrum, only contigs containing
       sequences from different	metagenomes are	kept; "pure" contigs are
       excluded. Additionally, the total number	of singletons (1-contigs) from
       each region that	assembles with any fragments from other	regions	is the
       number of 1-contigs in the cross	contig spectrum.

   Implementation
       The simplest representation of a	contig spectrum	is as a	hash
       representation where the	key is the contig size (number of sequences
       making up the contig) and the value the number of contigs of this size.

       In fact,	it is useful to	have more information associated with the
       contig spectrum,	hence the Bio::Assembly::Tools::ContigSpectrum module
       implements an object containing a contig	spectrum hash and additional
       information. The	get/set	methods	to access them are:

	   id		   contig spectrum ID
	   nof_rep	   number of repetitions (assemblies) used
	   max_size	   size	of (number of sequences	in) the	largest	contig
	   spectrum	   hash	representation of a contig spectrum

	   nof_seq	   number of sequences
	   avg_seq_len	   average sequence length

	   eff_asm_params  reports effective assembly parameters

	   nof_overlaps	   number of overlaps (needs eff_asm_params)
	   min_overlap	   minimum overlap length in a contig (needs eff_asm_params)
	   min_identity	   minimum sequence identity percentage	(needs eff_asm_params)
	   avg_overlap	   average overlap length (needs eff_asm_params)
	   avg_identity	   average overlap identity percentage (needs eff_asm_params)

	 Operations on the contig spectra:

	   to_string	   create a string representation of the spectrum
	   spectrum	   import a hash contig	spectrum
	   assembly	   determine a contig spectrum from an assembly, contig	or singlet
	   dissolve	   calculate a dissolved contig	spectrum (depends on assembly)
	   cross	   produce a cross contig spectrum (depends on assembly)
	   add		   add a contig	spectrum to an existing	one
	   average	   make	an average of several contig spectra
	   score	   score a contig spectrum: the	higher the number of contigs
			     and the larger their size,	the higher the score.

       When using operations that rely on knowing "where" (from	what
       metagenomes) a sequence came from (i.e. when creating a dissolved or
       cross contig spectrum), make sure that the sequences used for the
       assembly	have a name header, e.g.  >metagenome1|seq1,
       >metagenome2|seq1, ...

       Note: The following operations require the "Graph::Undirected" module:
	  eff_asm_params, cross, dissolve

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 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 email
       or the web:

	 bioperl-bugs@bio.perl.org
	 https://github.com/bioperl/bioperl-live/issues

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	 : my $csp = Bio::Assembly::Tools::ContigSpectrum->new();
		     or
		   my $csp = Bio::Assembly::Tools::ContigSpectrum->new(
		     -id => 'some_name',
		     -spectrum =>  { 1 => 90 , 2 => 3 ,	4 => 1 },
		   );
		     or
		   my $csp = Bio::Assembly::Tools::ContigSpectrum->new(
		     -assembly =>  $assembly_obj
		   );
	 Function: create a new	contig spectrum	object
	 Returns : reference to	a contig spectrum object
	 Args	 : none

   id
	 Title	 : id
	 Usage	 : $csp->id
	 Function: get/set contig spectrum id
	 Returns : string
	 Args	 : string [optional]

   nof_seq
	 Title	 : nof_seq
	 Usage	 : $csp->nof_seq
	 Function: get/set the number of sequences making up the contig	spectrum
	 Returns : integer
	 Args	 : integer [optional]

   nof_rep
	 Title	 : nof_rep
	 Usage	 : $csp->nof_rep
	 Function: Get/Set the number of repetitions (assemblies) used to create the
		   contig spectrum
	 Returns : integer
	 Args	 : integer [optional]

   max_size
	 Title	 : max_size
	 Usage	 : $csp->max_size
	 Function: get/set the size of (number of sequences in)	the largest contig
	 Returns : integer
	 Args	 : integer [optional]

   nof_overlaps
	 Title	 : nof_overlaps
	 Usage	 : $csp->nof_overlaps
	 Function: Get/Set the number of overlaps in the assembly.
	 Returns : integer
	 Args	 : integer [optional]

   min_overlap
	 Title	 : min_overlap
	 Usage	 : $csp->min_overlap
	 Function: get/set the assembly	minimum	overlap	length
	 Returns : integer
	 Args	 : integer [optional]

   avg_overlap
	 Title	 : avg_overlap
	 Usage	 : $csp->avg_overlap
	 Function: get/set the assembly	average	overlap	length
	 Returns : decimal
	 Args	 : decimal [optional]

   min_identity
	 Title	 : min_identity
	 Usage	 : $csp->min_identity
	 Function: get/set the assembly	minimum	overlap	identity percent
	 Returns : 0 < decimal < 100
	 Args	 : 0 < decimal < 100 [optional]

   avg_identity
	 Title	 : avg_identity
	 Usage	 : $csp->avg_identity
	 Function: get/set the assembly	average	overlap	identity percent
	 Returns : 0 < decimal < 100
	 Args	 : 0 < decimal < 100 [optional]

   avg_seq_len
	 Title	 : avg_seq_len
	 Usage	 : $csp->avg_seq_len
	 Function: get/set the assembly	average	sequence length
	 Returns : avg_seq_len
	 Args	 : real	[optional]

   eff_asm_params
	 Title	 : eff_asm_params
	 Usage	 : $csp->eff_asm_params(1)
	 Function: Get/set the effective assembly parameters option. It	defines	if the
		   effective assembly parameters should	be determined when a contig
		   spectrum based or derived from an assembly is calculated. The
		   effective assembly parameters include avg_seq_length, nof_overlaps,
		   min_overlap,	avg_overlap, min_identity and avg_identity.
		   1 = get them, 0 = don't.
	 Returns : integer
	 Args	 : integer [optional]

   spectrum
	 Title	 : spectrum
	 Usage	 : my $spectrum	= $csp->spectrum({1=>10, 2=>2, 3=>1});
	 Function: Get the current contig spectrum represented as a hash / Update a
		   contig spectrum object based	on a contig spectrum represented as a
		   hash
		   The hash representation of a	contig spectrum	is as following:
		     key   -> contig size (in number of	sequences)
		     value -> number of	contigs	of this	size
	 Returns : contig spectrum as a	hash reference
	 Args	 : contig spectrum as a	hash reference [optional]

   assembly
	 Title	 : assembly
	 Usage	 : my @obj_list	= $csp->assembly();
	 Function: get/set the contig spectrum object by adding	an assembly, contig or
		   singlet object to it, or get	the list of objects associated with it
	 Returns : arrayref of assembly, contig	and singlet objects used in the	contig
		   spectrum object (Bio::Assembly::Scaffold, Bio::Assembly::Contig and
		   Bio::Assembly::Singlet objects)
	 Args	 : Bio::Assembly::Scaffold, Contig or Singlet object

   drop_assembly
	 Title	 : drop_assembly
	 Usage	 : $csp->drop_assembly();
	 Function: Remove all assembly objects associated with a contig	spectrum.
		   Assembly objects can	take a lot of memory, which can	be freed by
		   calling this	method.	Don't call this	method if you need the assembly
		   object later	on, for	example	for creating a dissolved or cross
		   contig spectrum.
	 Returns : 1 for success
	 Args	 : none

   dissolve
	 Title	 : dissolve
	 Usage	 : $dissolved_csp->dissolve($mixed_csp,	$seq_header);
	 Function: Dissolve a mixed contig spectrum for	the set	of sequences that
		   contain the specified header, i.e. determine	the contribution of
		   these sequences to the mixed	contig spectrum. The mixed contig
		   spectrum object must	have one or several assembly object(s).	In
		   addition, min_overlap, min_identity and eff_asm_params are taken
		   from	the mixed contig spectrum, unless they are specified manually
		   for the dissolved contig spectrum. The dissolved contigs underlying
		   the contig spectrum can be obtained by calling the assembly() method.
	 Returns : 1 for success
	 Args	 : Bio::Assembly::Tools::ContigSpectrum	reference
		   sequence header string

   cross
	 Title	 : cross
	 Usage	 : $cross_csp->cross($mixed_csp);
	 Function: Calculate a cross contig_spectrum based on a	mixed contig_spectrum.
		   The underlying cross-contigs	themselves can be obtained by calling
		   the assembly() method.
	 Returns : 1 for success
	 Args	 : Bio::Assembly::Tools::ContigSpectrum	reference

   to_string
	 Title	 : to_string
	 Usage	 : my $csp_string = $csp->to_string;
	 Function: Convert the contig spectrum into a string (easy to print!!).
	 Returns : string
	 Args	 : element separator (integer) [optional]
		     1 -> space-separated
		     2 -> tab-separated
		     3 -> newline-separated

   add
	 Title	 : add
	 Usage	 : $csp->add($additional_csp);
	 Function: Add a contig	spectrum to an existing	one: sums the spectra, update
		   the number of sequences, number of repetitions, ...
	 Returns : 1 for success
	 Args	 : Bio::Assembly::Tools::ContigSpectrum	object

   average
	 Title	 : average
	 Usage	 : my $avg_csp = $csp->average([$csp1, $csp2, $csp3]);
	 Function: Average one contig spectrum or the sum of several contig spectra by
		   the number of repetitions
	 Returns : Bio::Assembly::Tools::ContigSpectrum
	 Args	 : Bio::Assembly::Tools::ContigSpectrum	array reference
		   eff_asm_params

   score
	 Title	 : score
	 Usage	 : my $score = $csp->score();
	 Function: Score a contig spectrum (or cross-contig spectrum) such that	the
		    higher the number of contigs (or cross-contigs) and	the larger their
		    size, the higher the score.
		    Let	n   : total number of sequences
			c_q : number of	contigs	of size	q
			q   : number of	sequence in a contig
		    We define: score = n/(n-1) * (X - 1/n)
			 where X = sum ( c_q * q^2 ) / n**2
		    The	score ranges from 0 (singlets only) to 1 (a single large contig)
		    It is possible to specify a	value for the number of	sequences to
		     assume in the contig spectrum.
	 Returns : contig score, or undef if there were	no sequences in	the contig spectrum
	 Args	 : number of total sequences to	assume [optional]

   _naive_assembler
	 Title	 : _naive_assembler
	 Usage	 :
	 Function: Reassemble the specified sequences only based on their position in
		   the contig. This naive assembly only	verifies that the minimum
		   overlap length and percentage identity are respected. No actual
		   alignment is	done
	 Returns : arrayref of contigs and singlets
	 Args	 : Bio::Assembly::Contig
		   array reference of sequence IDs to use [optional]
		   minimum overlap length (integer)	  [optional]
		   minimum percentage identity (integer)  [optional]

   _create_subcontig
	 Title	 : _create_subcontig
	 Usage	 :
	 Function: Create a subcontig from another contig
	 Returns : Bio::Assembly::Contig object
	 Args	 : Bio::Assembly::Contig
		   arrayref of the IDs of the reads to includes	in the subcontig
		   ID to give to the subcontig

   _obj_copy
	 Title	 : _obj_copy
	 Usage	 :
	 Function: Copy	(most of) an object, and optionally truncate it
	 Returns : another a Bio::LocatableSeq,	Bio::Seq::PrimaryQual, or
		     Bio::SeqFeature::Generic object
	 Args	 : a Bio::LocatableSeq,	Bio::Seq::PrimaryQual, or
		     Bio::SeqFeature::Generic object
		   a start position
		   an end position

   _new_from_assembly
	 Title	 : _new_from_assembly
	 Usage	 :
	 Function: Creates a new contig	spectrum object	based solely on	the result of
		   an assembly,	contig or singlet
	 Returns : Bio::Assembly::Tools::ContigSpectrum	object
	 Args	 : Bio::Assembly::Scaffold, Contig or Singlet object

   _new_dissolved_csp
	 Title	 : _new_dissolved_csp
	 Usage	 :
	 Function: create a dissolved contig spectrum object
	 Returns : dissolved contig spectrum
	 Args	 : mixed contig	spectrum
		   header of sequences to keep in this contig spectrum

   _dissolve_contig
	 Title	 : _dissolve_contig
	 Usage	 :
	 Function: dissolve a contig
	 Returns : arrayref of contigs and singlets
	 Args	 : mixed contig	spectrum
		   header of sequences to keep in this contig spectrum
		   minimum overlap
		   minimum identity

   _new_cross_csp
	 Title	 : _new_cross_csp
	 Usage	 :
	 Function: create a cross contig spectrum object
	 Returns : cross-contig	spectrum
	 Args	 : mixed contig	spectrum

   _cross_contig
	 Title	 : _cross_contig
	 Usage	 :
	 Function: calculate cross contigs
	 Returns : arrayref of cross-contigs
		   number of cross-singlets
	 Args	 : contig
		   minimum overlap
		   minimum identity

   _seq_origin
	 Title	 : _seq_origin
	 Usage	 :
	 Function: determines where a sequence comes from using	its header. For	example
		   the origin of the sequence 'metagenome1|gi|9626988|ref|NC_001508.1|'
		   is 'metagenome1'
	 Returns : origin
	 Args	 : sequence ID

   _import_assembly
	 Title	 : _import_assembly
	 Usage	 : $csp->_import_assembly($assemblyobj);
	 Function: Update a contig spectrum object based on an assembly, contig	or
		   singlet object
	 Returns : 1 for success
	 Args	 : Bio::Assembly::Scaffold, Contig or Singlet object

   _import_spectrum
	 Title	 : _import_spectrum
	 Usage	 : $csp->_import_spectrum({ 1 => 90 , 2	=> 3 , 4 => 1 })
	 Function: update a contig spectrum object based on a contig spectrum
		   represented as a hash (key: contig size, value: number of contigs of
		   this	size)
	 Returns : 1 for success
	 Args	 : contig spectrum as a	hash reference

   _import_dissolved_csp
	 Title	 : _import_dissolved_csp
	 Usage	 : $csp->_import_dissolved_csp($mixed_csp, $seq_header);
	 Function: Update a contig spectrum object by dissolving a mixed contig
		   spectrum based on the header	of the sequences
	 Returns : 1 for success
	 Args	 : Bio::Assembly::Tools::ContigSpectrum
		   sequence header string

   _import_cross_csp
	 Title	 : _import_cross_csp
	 Usage	 : $csp->_import_cross_csp($mixed_csp);
	 Function: Update a contig spectrum object by calculating the cross contig
		   spectrum based on a mixed contig spectrum
	 Returns : 1 for success
	 Args	 : Bio::Assembly::Tools::ContigSpectrum

   _get_contig_like
	 Title	 : _get_contig_like
	 Usage	 : my @contig_like_objs	= $csp->_get_contig_like($assembly_obj);
	 Function: Get contigs and singlets from an assembly, contig or	singlet
	 Returns : array of Bio::Assembly::Contig and Singlet objects
	 Args	 : a Bio::Assembly::Scaffold, Contig or	singlet	object

   _get_assembly_seq_stats
	 Title	 : _get_assembly_seq_stats
	 Usage	 : my $seqlength = $csp->_get_assembly_seq_stats($assemblyobj);
	 Function: Get sequence	statistics from	an assembly:
		     average sequence length, number of	sequences
	 Returns : average sequence length (decimal)
		   number of sequences (integer)
	 Args	 : Bio::Assembly::Scaffold, Contig or singlet object
		   hash	reference with the IDs of the sequences	to consider [optional]

   _get_contig_seq_stats
	 Title	 : _get_contig_seq_stats
	 Usage	 : my $seqlength = $csp->_get_contig_seq_stats($contigobj);
	 Function: Get sequence	statistics from	a contig:
		     average sequence length, number of	sequences
	 Returns : average sequence length (decimal)
		   number of sequences (integer)
	 Args	 : contig object reference
		   hash	reference with the IDs of the sequences	to consider [optional]

   _update_seq_stats
	 Title	 : _update_seq_stats
	 Usage	 :
	 Function: Update the number of	sequences and their average length 1
		   average identity 1
		   minimum length 1
		   minimum identity 1
		   number of overlaps 1	average	sequence length
	 Returns : average sequence length
		   number of sequences
	 Args	 : average sequence length 1
		   number of sequences 1
		   average sequence length 2
		   number of sequences 2

   _get_assembly_overlap_stats
	 Title	 : _get_assembly_overlap_stats
	 Usage	 : my ($avglength, $avgidentity, $minlength, $min_identity, $nof_overlaps)
		     = $csp->_get_assembly_overlap_stats($assemblyobj);
	 Function: Get statistics about	pairwise overlaps in contigs of	an assembly
	 Returns : average overlap length
		   average identity percent
		   minimum overlap length
		   minimum identity percent
		   number of overlaps
	 Args	 : Bio::Assembly::Scaffold, Contig or Singlet object
		   hash	reference with the IDs of the sequences	to consider [optional]

   _get_contig_overlap_stats
	 Title	 : _get_contig_overlap_stats
	 Usage	 : my ($avglength, $avgidentity, $minlength, $min_identity, $nof_overlaps)
		     = $csp->_get_contig_overlap_stats($contigobj);
	 Function: Get statistics about	pairwise overlaps in a contig or singlet. The
		     statistics	are obtained using graph theory: each read is a	node
		     and the edges between 2 reads are weighted	by minus the number of
		     conserved residues	in the alignment between the 2 reads. The
		     minimum spanning tree of this graph represents the	overlaps that
		     form the contig. Overlaps that do not satisfy the minimum overlap
		     length and	similarity get a malus on their	score.
		     Note: This	function requires the optional BioPerl dependency
		     module called 'Graph'
	 Returns : average overlap length
		   average identity percent
		   minimum overlap length
		   minimum identity percent
		   number of overlaps
	 Args	 : Bio::Assembly::Contig or Singlet object
		   hash	reference with the IDs of the sequences	to consider [optional]

   _update_overlap_stats
	 Title	 : _update_overlap_stats
	 Usage	 :
	 Function: update the number of	overlaps and their minimum and average length
		   and identity
	 Returns :
	 Args	 : average length 1
		   average identity 1
		   minimum length 1
		   minimum identity 1
		   number of overlaps 1
		   average length 2
		   average identity 2
		   minimum length 2
		   minimum identity 2
		   number of overlaps 2

   _overlap_alignment
	 Title	 : _overlap_alignment
	 Usage	 :
	 Function: Produce an alignment	of the overlapping section of two sequences of
		   a contig. Minimum overlap length and	percentage identity can	be
		   specified. Return undef if the sequences do not overlap or do not
		   meet	the minimum overlap criteria.
	 Return	 : Bio::SimpleAlign object reference
		   alignment overlap length
		   alignment overlap identity
	 Args	 : Bio::Assembly::Contig object	reference
		   Bio::LocatableSeq contig sequence 1
		   Bio::LocatableSeq contig sequence 2
		   minium overlap length [optional]
		   minimum overlap identity percentage[optional]

   _contig_graph
	 Title	 : _contig_graph
	 Usage	 :
	 Function: Creates a graph data	structure of the contig.The graph is undirected.
		   The vertices	are the	reads of the contig and	edges are the overlap
		   between the reads. The edges	are weighted by	the opposite of	the
		   overlap, so it is negative and the better the overlap, the lower the
		   weight.
	 Return	 : Graph object	or undef
		   hashref of overlaps (score, length, identity) for each read pair
	 Args	 : Bio::Assembly::Contig object	reference
		   hash	reference with the IDs of the sequences	to consider [optional]
		   minimum overlap length (integer)			    [optional]
		   minimum percentage identity (integer)		    [optional]

   _draw_graph
	 Title	 : _draw_graph
	 Usage	 :
	 Function: Generates a PNG picture of the contig graph.	It is mostly for
		   debugging purposes.
	 Return	 : 1 for success
	 Args	 : a Graph object
		   hashref of overlaps (score, length, identity) for each read pair
		   name	of output file
		   overlap info	to display: 'score' (default), 'length'	or 'identity'

perl v5.24.1			  2017-Bio::Assembly::Tools::ContigSpectrum(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Florent E Angly | APPENDIX

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