To specify read technology in the Input Sequences screen, make a selection from the Read technology drop-down menu. Default values for parameters and other assembly options in subsequent panels will be based on this selection.

Considerations when choosing a read technology:

  • If you are following a long-read workflow, the only options are PacBio (Pacific Biosciences) or ONT (Oxford Nanopore Technologies).
  • If you choose Illumina, SeqMan NGen assumes that you have paired-end data > 50 bp in length, and with a 500 bp insert distance. For all other technologies, SeqMan NGen presumes single-end data. If the read length is shorter than 50 bp, you may wish to specify a shorter Mer size in the Assembly Options screen. When using very short reads, you may also consider optimizing the Minimum aligned length and Maximum gap size in the Alignment tab.
  • For de novo workflows, if you select Illumina and enter an insert size of 150 bp or less in the Set Pair Information dialog, the assembler will assume the reads overlap and will attempt to create a single “super-read” from each pair. Read pairs that cannot be merged, either because they do not overlap or have numerous errors in the overlapping region, will not be included in the assembly. See Remove PhiX control reads from Illumina data prior to import for a description of how to use Contaminant scan to remove PhiX174 control sequence from Illumina data prior to assembly.
  • Both types of Ion Torrent paired reads—”mate pairs” and “paired ends”—are supported.
  • If using both Sanger and Illumina data, choose Illumina for all reads.

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