The setPairSpecifier command defines the paired end pair specifier for the paired Sanger and Illumina sequences in the assembly. This command must appear in the script before the assemble command, but after sequences have been loaded using the loadSeq command. For more information on assembling 454 paired end data, see the load454PairedEnd command. Pair specifiers define the naming convention for sequence pairs, as well as requirements for a minimum and maximum distance between the opposite ends of the inserts. Expressions for forward and reverse naming conventions should be created using the paired end specification language. Forward and reverse sequences must have identical names except for the unique portion that determines the direction of the clone.

Parameter Description Allowed values
pairs This parameter lists the paired end constraints, specified by the following four values. Each value should be separated by a space and the list of values enclosed in double brackets {}. An additional set of brackets is required around all of the paired end constraints, regardless of whether one or multiple pair constraints are specified. [forward|reverse|min|max]
forward A naming pattern to match forward clones. [text string enclosed in quotes]
max The maximum distance for the paired end sequences to be separated. [number]
min The minimum distance for the paired end sequences to be separated. [number]
reverse A naming pattern to match reverse clones. [text string enclosed in quotes]


(defines 2 pair specifiers each with different size ranges)

   pairs:{{forward:”(.*)(2kb)(.*)-FP.*$”reverse:”(.*)(2kb)(.*)-RP.*$” min: 1500 max: 2500}
     {forward:”(.*)(8kb)(.*)-FP.*$” reverse:”(.*)(8kb)(.*)-RP.*$” min: 7000 max: 9000}}

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