Import NGS Reads
CLC Genomics Workbench has dedicated importers for next-generation sequencing (NGS) reads, both short and long7.1, described in the following sections.
Click on the Import () button in the top toolbar to bring up a list of available importers, as shown in figure 7.7. Click on the importer to launch it.
Figure 7.7: Importers for NGS short and long reads.
To specify the files to import, click:
- Add folders to choose one or several folders from which all the files should be imported.
- Add files to select individual files to import.
Files can be removed from the list by selecting them and clicking the Remove button.
The Element Info () view of the imported element(s) shows and can be used to edit:
- The read group platform, which is determined by the importer, see figure 7.8.
- The paired status, see General notes on handling paired data.
Figure 7.8: Editing the platform in the Element Info view.
Fastq importers can process UMI information from the fastq read headers, see General notes on UMIs.
Footnotes
Subsections
- Illumina
- Oxford Nanopore
- PacBio Long Reads
- PacBio Onso
- Element Biosciences
- Ion Torrent
- MGI/BGI
- Singular Genomics
- Ultima Genomics
- General notes on handling paired data
- General notes on UMIs