Import high-throughput sequencing data

The Biomedical Genomics Workbench has dedicated tools for importing data from the following High-throughput sequencing systems.

Importers for Roche 454 and SOLiD are also available in the Legacy Tools folder.

The reason for having dedicated tools for this is to standardize the data so that most downstream analyses and visualization of the data works seamlessly with all sequencing platforms. In case a sequence list was not imported with the right tool, it is possible to edit "Read Group" information in the "Element Info" view: choose from the drop-down menu the sequencing platform that was used to generate the data (figure 6.7) and click OK.

Image editplatform
Figure 6.7: Editing the platform that was used to generate the data in the "Element Info" view.

In addition to these formats, mapped data in SAM/BAM format can also be imported.

Clicking on the Import (Image Next_Folder_16_n_p) button in the top toolbar will bring up a list of the supported data types as shown in figure 6.8.

Image importngsdialogGW7
Figure 6.8: Choosing what kind of data you wish to import.

Select the appropriate format and then fill in the information as explained in the following sections.

Please note that alignments of Complete Genomics data can be imported using the Complete Genomics import.