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. |
[IonTorrent|SOLiD|Illumina|454|normalScore|Other] |
| templateFragment | Used in reference-guided assemblies with gap closure. | [number] |
Example:
loadSeq
file: “/Library/ABC_project/ABC_sequences.fas”
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