Introducing the MiniSeq Rapid Reagent Kit

What's New:

• The MiniSeq Rapid Reagent Kit (100 cycles) uses a new Rapid recipe enabled by an upgrade to MiniSeq Control Software v2.1.

• The Rapid recipe reduces the run time for a 1x101 bp non-indexed run to ~4.8 hours, making it ideal for applications that need a fast turnaround time.

• The MiniSeq Rapid recipe allows for dual-indexed single-read runs. To reduce run time, the i5 Index Read uses the forward strand indexing workflow, rather than the reverse strand workflow that is used with standard MiniSeq reagent kits. This workflow allows the second index to be sequenced without going through paired-end turnaround.

Frequently asked questions:

• How to download the MiniSeq Control Software v2.1? The software can be downloaded from BaseSpace Sequence Hub or from the MiniSeq System Software Download page. The software can only be installed on systems that have been upgraded to Windows 10. Contact your local field engineer or [e-mail] to upgrade a MiniSeq to Windows 10.

• What library prep kits are compatible with the MiniSeq Rapid reagent Kit This kit has been validated with the Illumina RNA Prep with Enrichment + Respiratory Virus Oligos Panel v2, using a 1x76 bp run length, as viewable in the BaseSpace Demo Data. However, this reagent kit is compatible with any library that uses a single-read length of 1x101 bp or less.

• Can we set up a paired-end run with the MiniSeq Rapid cartridge? No, MiniSeq Rapid is only compatible with single-read runs. Setting up a paired-end run will result in an error upon MiniSeq Rapid cartridge loading.

• What is the advantage of using the MiniSeq Rapid 100-cycle kit instead of the MiniSeq 75-cycle kit? The MiniSeq Rapid 100-cycle kit allows for a faster run time than the MiniSeq 75-cycle kit, and longer Read 1 length.

• How many cycles are in the kit? The MiniSeq Rapid 100-cycle kit includes 128 cycles of chemistry that is sufficient for a 1x101 bp Read 1 with 2x10 bp index reads, plus seven chemistry-only cycles before the Index 2 Read.

• Can standard MiniSeq reagent kits be used with MiniSeq Control Software v2.1? Yes, the MiniSeq Control Software v2.1 is backwards compatible and can be run with all available MiniSeq reagent kits. However, the Rapid Run recipe can only be used with the MiniSeq Rapid cartridge.

• What is the number of reads passing filter expected with the Rapid reagent kit? The MiniSeq Rapid Runs are expected to generate 20 million reads passing filter.

• Does the loading concentration change when using a Rapid reagent kit? Yes. If a library loading concentration has been optimized with MiniSeq standard reagent kits, we recommend increasing loading concentration by ~15% to achieve a similar cluster density to standard MiniSeq runs.

• What i5 index sequence orientation should be used for sample sheets? MiniSeq Rapid uses the forward strand orientation to read the i5 index. If setting up a Manual Run, make sure that the sample sheet lists the i5 index sequence in the forward orientation. If setting up a run in Local Run Manager, import a sample sheet with the i5 index sequence in reverse complement orientation. Local Run Manager automatically reverse complements the i5 index sequence back to the correct forward strand orientation.

Read length	Run time without index reads	Run time with single index	Run time with dual indexes
1 x 101 bp	4.7 hours	5.1 hours	5.7 hours
1 x 76 bp	3.7 hours	4.2 hours	4.8 hours
1 x 51 bp	2.8 hours	3.3 hours	3.9 hours
1 x 36 bp	2.3 hours	2.7 hours	3.3 hours

Table 1: Run time estimates with MiniSeq Rapid 100-cycle kit

Note: Estimated times are based on preliminary testing data. Actual run times may change depending on cluster density and available computer resources.

For any feedback or questions regarding this article (Illumina Knowledge Article #3743), contact Illumina Technical Support [e-mail].