How are PhiX reads processed by G4?

This article describes how data from the control library PhiX is handled during Primary Analysis on G4.

Sequencing runs are often spiked with PhiX to include a known control and increase read diversity. The Singular Genomics PhiX DNA Control is ready to sequence with dual barcoded indices that are outside of our set of 96 indices:

PhiX Index Read 1: AAGGTAGCTACA

PhiX Index Read 2: GACAACCTACCT

All insert reads coming out of the G4 Sequencing Platform are aligned against PhiX and reads mapping highly to PhiX are marked as a control read. The Singular Demultiplexer will remove the control reads as a default option. If you wish to keep the PhiX reads, set the --filter-control-reads option to false in the Singular Demuxer command line or from the Sample Sheet. You can also use the Singular Demuxer Workflow and set the "filter_control" option to false in the corresponding parameter file.

Additionally, include the PhiX indices in the Sample Data Sheet to assign the PhiX reads to their own sample. Otherwise, the PhiX reads will be demultiplexed into the undetermined FASTQ file during demultiplexing.