Considerations when migrating non Illumina libraries between sequencing platforms
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All libraries prepared with the current Illumina library preparation kits not requiring a custom sequencing primer are compatible with all Illumina sequencing platforms.
Sequencing libraries prepared with non-Illumina library preparation methods may require additional optimization on different sequencing platforms. Consider the following differences:
The iSeq 100, MiniSeq, MiSeq, MiSeq i100 Series, NextSeq 500/550, NextSeq 1000/2000, NovaSeq 6000, and NovaSeq X Series flow cells are paired-end.
Libraries with paired-end adapter designs can be run as single-read or paired-end sequencing runs, but some older single-read libraries may not sequence successfully on modern paired-end flow cells. As a result, it may not be possible to successfully sequence some libraries developed for single-read applications on the HiSeq 1000/1500/2000/2500 on the iSeq 100, MiniSeq, MiSeq, MiSeq i100 Series, NextSeq 500/550, NextSeq 1000/2000, NovaSeq 6000, or NovaSeq X Series.
For guidance on if a library has a single-read or paired-end adapter design, contact .
Primer Binding and SBS chemistry temperatures
Temperatures used for primer binding, deblocking, and nucleotide incorporation steps can vary between platforms and therefore need to be considered when using custom primer or primer binding sites.
Platform
Primer Binding
Deblocking
Incorporation
iSeq 100
65° C
63° C
65° C
MiniSeq
60° C
60° C
60° C
MiSeq
65° C
60° C
65° C
MiSeq i100 Series
65° C
56° C
65° C
NextSeq 500/550
60° C
60° C
60° C
NextSeq 1000/2000
60° C
60° C
60° C
NovaSeq 6000
60° C
55° C
60° C
NovaSeq X Series
60° C
60° C
60° C
Clustering efficiency
Libraries can exhibit different clustering efficiencies when migrating from one platform to another. Consult the bulletin, for additional information on these variations.
Additional considerations
Insert sizes more than 550 bp are generally not supported on the MiniSeq or NextSeq 500/550,and may require additional optimization steps.
Some applications with 550 bp or greater insert sizes are compatible with the NovaSeq 6000 platform, but additional optimization steps may be required.
Current versions of the MiSeq Control Software are optimized to run low diversity libraries. MiniSeq, NextSeq 500/550, NovaSeq 6000, and NovaSeq X Series software do not. For this reason, running low diversity libraries on these systems requires additional optimization.
For any feedback or questions regarding this article (Illumina Knowledge Article #1478), contact Illumina Technical Support .