Import of PacBio reads

Choosing the PacBio importer will open the dialog shown in figure 15.1.

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 15.1: Importing data from PacBio.

We support import of the following file formats containing PacBio reads:

Under General options you have the following choices:

Under PacBio options you find the following setting:

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.