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.
| Parameter | Description | Allowed values |
|---|---|---|
| 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] Default = 10000 |
| min, minDistance | The minimum distance for the paired end constraint. | [number] Default = 0 |
Example:
load454PairedEnd
file: “/Library/454 data/123_Pairedend.fas”
linker: “/Library/454 data/123_linkerseqs.fas”
min: 0
max: 10000
DiscardLinkerless: false
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