The splitPairs command is used to split 454 or ion torrent mate pair files into forward and reverse (and singleton) files.

Parameter Description Allowed value
destination The location and filename for the output. [directory/filename enclosed in quotes]
DiscardLinkerless Specifies that reads without a linker sequence should be discarded from the assembly. [ true / false ]
file, reads The location and filename for the input. [directory/filename enclosed in quotes]
seqTech Specifies the offset to be used when converting compressed quality scores into numerical values. These are the offsets used for the technology specified:

Data Type / Value / Offset
IonTorrent / IonTorrent / 33
Applied Biosystems SOLiD / SOLiD / 33
Illumina / Illumina / 64
Roche 454 / 454 / 33
Other types / normalScore / 33

Wizard equivalent: Input Sequence Files > Read technology.

Note 1: For 454,quality scores for homopolymeric runs of ≥ 2 are oriented from 5’ to 3’ on the top strand.

Note 2: If possible, the data type of unknown data is determined automatically based on the first data file.


reads: {
{ file:”C:data\reads\file1.fas” format: IonTorrent }
{ file: “C:data\reads\file2.fas” format:454 discardLinkerless: true}

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