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Sequencing of Open-ST library


We recommend quantifying your libraries for sequencing using the KAPA Library Quantification Kit.

Loading and sequencing

The optimal loading concentration depends on the sequencer used. For the Illumina® NovaSeq 6000 we obtained optimal clustering at a loading concentration of 130 pM. For the Illumina® NextSeq 2000 sequencing system we recommend a loading concentration of 650 pM.

Moreover, Illumina suggests a minimum spike-in of 1% PhiX into the pool as a quality control for cluster generation, sequencing, and alignment.

In our setup, the following read lengths were used:

Read Cycles
Read 1 28-32
Index 1 8
Index 2 NA
Read2 90+

Expected (data) output

Either when using your own sequencing equipment or relying on a sequencing facility, you will get access to (most likely) already demultiplexed fastq files; otherwise, you can get access to the raw basecall files in bcl format.

Either of these files shall be used as the input for spacemake later.