PacBio Long Reads

The PacBio Long Reads importer is designed to import long reads generated by PacBio sequencing technology.

To launch the PacBio Long Reads importer, go to:

        Import (Image Next_Folder_16_n_p) | PacBio (Image color_ngs_import_16_n_p) | PacBio Long Reads (Image color_ngs_import_16_n_p).

This opens a dialog where files can be selected and import options specified (figure 7.10).

Note: PacBio HiFi reads are not fully supported. Of particular note: Tools that carry out de novo assembly do not support this data type, and quality scores are capped at 64, affecting tools that make use of such scores, e.g. variant detection tools.

Image import_pacbio_files
Figure 7.10: Importing data from PacBio.

The following file formats are supported:

The General options are:

The PacBio options are:

Click Next and choose how the result of the import should be handled. We recommend choosing Save which will save the results directly to the disk.

Mark imported PacBio reads as HiFi

To mark already imported PacBio reads as PacBio HiFi, change the so-called "Read group" value for the imported sequence list:

  1. Open the sequence list in the View Area.
  2. Click on the "Show Element Info" icon (Image element_info_16_n_p) found at the bottom of the window.
  3. Click on Edit next to Read group.
  4. In the Platform dropdown, change from PACBIO to PACBIO_HIFI.
  5. Click on OK.