The loadSeq command loads a sequence file or files for assembly. See our website for a list of supported file types.
|blockContig||Used in the reference-guided workflow.||[text string]|
|blockContigID||Used in the reference-guided workflow.||[number]|
|blockName||Used in the reference-guided workflow.||[text string]|
|blockPos||Used in the reference-guided workflow.||[number]|
|DiscardLinkerless||Specifies whether reads that do not have a linker sequence should be discarded from the assembly.||[ true / ]|
|file||(required) Specifies the directory and file name of the sequence file(s) to be loaded. A folder may also be specified, in which case all of the sequence files within that folder will be loaded.||[directory/filename enclosed in quotes]|
|groupName||Used to identify the multi-sample group name for a read file.||[text string]|
|isPair||Specifies whether the query files contain paired end data.||[ true / ]|
|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||The maximum distance for the paired end constraint.|| [number]
|maxSeqs||Specifies the maximum number of reads to load from a file.||[number]|
|mergePairs||Specifies whether the reads are paired end data that overlap and should therefore be merged.||[ true / ]|
|min||The minimum distance for the paired end constraint.|| [number]
|minSeqLen||Minimum length of a sequence required to include it in the assembly.||[number]|
|multiplex||Specifies whether reads are from a multi-sample run.||[ true / ]|
|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
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.
|templateFragment||Used in reference-guided assemblies with gap closure.||[number]|
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