The loadSeq command loads a sequence file or files for assembly. See our website for a list of supported file types.

Parameter Description Allowed values
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 / false ]
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 / false ]
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]

Default = 10000
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 / false ]
min The minimum distance for the paired end constraint. [number]

Default = 0
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 / false ]
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]


   file: “/Library/ABC_project/ABC_sequences.fas”

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