Title : new
Usage : $factory = Bio::Tools::Run::Phrap->new(
-penalty => -2, # parameter option and value
-raw => 1 # flag (1=yes, 0=no)
Function: Create a new Phrap factory
Returns : A Bio::Tools::Run::Phrap object
Args : Phrap options available in this module:
Option names & default values taken from the PHRAP manual:
1. Scoring of pairwise alignments
Mismatch (substitution) penalty for SWAT comparisons.
Gap initiation penalty for SWAT comparisons.
Gap extension penalty for SWAT comparisons.
Insertion gap extension penalty for SWAT comparisons (insertion in
subject relative to query).
Deletion gap extension penalty for SWAT comparisons (deletion in
subject relative to query).
Score matrix for SWAT comparisons (if present, supersedes -penalty)
Use raw rather than complexity-adjusted Smith-Waterman scores.
2. Banded search
Maximum length of matching word. For cross_match, the default value
is equal to minmatch, instead of 30.
Group size (query file, forward strand words)
Use raw rather than complexity-adjusted word length, in testing
against minmatch (N.B. maxmatch always refer to raw lengths). (The
default is to adjust word length to reflect complexity of matching
1/2 band width for banded SWAT searches (full width is 2 times
bandwidth + 1). Decreasing bandwidth also decreases running time at
the expense of sensitivity. Phrap assemblies of clones containing long
tandem repeats of a short repeat unit (< 30 bp) may be more accurately
assembled by decreasing -bandwidth; -bandwidth should be set such that
2 bandwidth + 1 is less than the length of a repeat unit. -bandwidth 0
can be used to find gap-free alignments.
3. Filtering of matches
Minimum alignment score.
Number of potential vector bases at beginning of each read. Matches
that lie entirely within this region are assumed to represent vector
matches and are ignored. For cross_match, the default value is 0
instead of 80.
(cross_match only). A match is reported only if at least (100 -
masklevel)% of the bases in its "domain" (the part of the query that
is aligned) are not contained within the domain of any higher-scoring
-masklevel 0 report only the single highest scoring match for each query
-masklevel 100 report any match whose domain is not completely contained
within a higher scoring match
-masklevel 101 report all matches
4. Input data interpretation
Quality value to be used for each base, when no input .qual file is
provided. Note that a quality value of 15 corresponds to an error rate
of approximately 1 in 30 bases, i.e. relatively accurate sequence. If
you are using sequence that is substantially less accurate than this
and do not have phred-generated quality values you should be sure to
decrease the value of this parameter.
(phrap only). Subclone name delimiter: Character used to indicate end
of that part of the read name that corresponds to the subclone name
(phrap only). Indicates which occurrence of the subclone delimiter
character denotes the end of the subclone name (so for example
-subclone_delim _ -n_delim 2
means that the end of the subclone name occurs at the
second occurrence of the character _). Must be the same for all
(phrap only). Group name delimiter: Character used to indicate end of
that part of the read name that corresponds to the group name
(relevant only if option -preassemble is used); this character must
occur before the subclone delimiter (else it has no effect, and the
read is not assigned to a group).
(phrap only). No. of bases to be removed at beginning of each read.
(phrap only). Relaxes stringency to varying degree during final
contig merge pass. Allowed values are integers from 0 (most
stringent) to 10 (least stringent), inclusive.
(phrap only). Controls treatment of inconsistent reads in merge.
Currently allowed values are 0 (no bypasses allowed; most stringent)
and 1 (a single conflicting read may be bypassed).
(phrap only). Maximum permitted size of an unmatched region in
merging contigs, during first (most stringent) merging pass.
(phrap only). Controls stringency of match required for joins. Must
be less than 1 (highest stringency), and greater than 0 (lowest
(phrap only). Splits initial greedy assembly into pieces at "weak
joins", and then tries to reattach them to give higher overall score.
Use of this option should correct some types of missassembly.
(phrap only). Breaks assembly at weak joins (as with -revise_greedy)
but does not try to reattach pieces.
(phrap only). Preassemble reads within groups, prior to merging with
other groups. This is useful for example when the input data set
consists of reads from two distinct but overlapping clones, and it is
desired to assemble the reads from each clone separately before
merging in order to reduce the risk of incorrect joins due to
repeats. The preassemble merging pass is relatively stringent and not
guaranteed to merge all of the reads from a group.
Groups are indicated by the first part of the read name, up to the
character specified by -group_delim.
(phrap only). Causes edited high-quality discrepancies to be ignored
during final contig merge pass. This option may be useful when it is
suspected that incorrect edits are causing a misassembly.
6. Consensus sequence construction
(phrap only). Minimum segment size (for purposes of traversing
weighted directed graph).
(phrap only). Spacing between nodes (in weighted directed graph).
Not implemented in this Perl module.
(phrap only). Retain exact duplicate reads, rather than eliminating
(phrap only). Maximum subclone size -- for forward-reverse read pair
(phrap only). Penalty used for identifying degenerate sequence at
beginning & end of read.
(phrap only). Minimum score for identifying degenerate sequence at
beginning & end of read.
(phrap only). Quality value used in to define the "high-quality" part
of a read, (the part which should overlap; this is used to adjust
qualities at ends of reads.
(phrap only). Minimum size of confirming segment (segment starts at
3d distinct nuc following discrepancy).
(phrap only). Amount by which confirming segments are trimmed at
(phrap only). Penalty used in aligning against "confirming" reads.
(phrap only). Minimum alignment score for a read to be allowed to
"confirm" part of another read.
Size of indexing (hashing) words, used in finding word matches
between sequences. The value of this parameter has a generally minor
effect on run time and memory usage.