Ion Torrent
The Ion Torrent importer is designed to import files generated by Ion Torrent sequencing technology.
To launch the Ion Torrent importer, go to:
Import (
) | Other NGS Reads (
) | Ion Torrent ().
This opens a dialog where files can be selected and import options specified (figure 7.13).
Figure 7.13: Importing data from Ion Torrent.
The following file formats are supported:
- SFF (
.sff). Can provide extra information about adapter regions or regions of low quality. - Fastq (
.fastq/.fq). Uncompressed files as well as files compressed using gzip (.gz), zip (.zip) or bzip2 (.bz2) can be provided as input. Quality scores are expected to be in the NCBI/Sanger format, see Quality scores in the Illumina platform. The importer processes UMI information from the fastq read headers, see General notes on UMIs. - SAM or BAM (
.sam/.bam). Mapping information in the file is disregarded.
The General options are:
- Discard read names. Read names can be discarded to save disk space without affecting analysis results. Keeping read names can be useful in some circumstances, such as when inspecting sequence list contents or when working downstream with subsets of sequences.
- Discard quality scores. Quality scores are visible in read mappings and are used by various tools, e.g. for variant detection. If quality scores are not relevant, use this option to discard them and reduce disk space and memory consumption.
The Ion Torrent options are:
- Use clipping information. Choose if clipping information in the sff format files should be used.