The load454PairedEnd command loads a file of Roche 454 sequences and checks for the presence of a linker defining the paired end sequences. If the linker is found, the linker is removed and the remaining portion is split into two sequences linked with a paired end constraint.
|DiscardLinkerless||Specifies whether to discard any read where no portion of the mate pair linker was found. In this way, reads that do not have a linker sequence will be discarded from the assembly.||[true|false]|
|file||The directory and file name of the .fas, .fna, or .sff file containing the 454 sequences.||[directory/filename enclosed in quotes]|
|linker||The directory and file name of the .fas, fna, or .sff file containing the 454 linker sequences. If not specified, SeqMan NGen will use its default 454 linker sequence: GTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAAC.||[directory/filename enclosed in quotes]|
|max, maxDistance||The maximum distance for the paired end constraint.|| [number]
|min, minDistance||The minimum distance for the paired end constraint.|| [number]
file: “/Library/454 data/123_Pairedend.fas”
linker: “/Library/454 data/123_linkerseqs.fas”
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