What is read length? Sequence read length refers to the length of each sequenced DNA fragment and whether it is sequenced from one end or both ends. For example, a 2 × 150 bp run generates two reads (forward and reverse) of 150 base pairs for each DNA fragment. Longer read lengths have a better probability of spanning repeats in the DNA sequence, while shorter read lengths can be cost-effective for counting methodologies where broad genome coverage is not required.
MiSeq i100 Series specifications
Fast and flexible sequencing
Short run times, scalable output, and exceptional data quality
Output per flow cell for various read lengthsa
| Flow cell type | 5Mb | 25Mb | 50Mc | 100Mc |
|---|---|---|---|---|
| 1 × 100 bp | — | 2.5 Gb | 5 Gb | 10 Gb |
| 2 × 150 bp | 1.5 Gb | 7.5 Gb | 15 Gb | 30 Gb |
| 2 x 300 bp | 3 Gb | 15 Gb | 30 Gb | — |
a. Specifications based on Illumina PhiX control library at supported cluster densities.
b. 5M and 25M flow cells available now.
c. 50M and 100M flow cells will be available starting in 2025 for the MiSeq i100 Plus System only.
Reads passing filter per flow cell
What are reads passing filter? The percentage of clusters passing chastitya filtering, with each passing filter cluster providing a read (single-end reads) or two reads (paired-end reads). Clusters pass filter if no more than one base call has a chastity value below 0.6 in the first 25 cycles. Single-end runs involve sequencing DNA from only one end and offer an economical alternative. Paired-end runs sequence both DNA ends for easier analysis of rearrangements, novel transcripts, and more.
| Flow cell type | 5Mb | 25Mb | 50Mc | 100Mc |
|---|---|---|---|---|
| Single reads | 5M | 25M | 50M | 100M |
| Paired-end reads | 10M | 50M | 100M | 200M |
a. Chastity is defined as the ratio of the brightest base intensity divided by the sum of the brightest and second brightest base intensities.
b. 5M and 25M flow cells available now.
c. 50M and 100M flow cells will be available starting in 2025 for the MiSeq i100 Plus System only.
Quality scoresa
What is a quality score? A quality score, or Q score, is a prediction of the probability of an error in base calling. Higher Q scores indicate a smaller probability of error. A quality score of 30 represents an error rate of one in 1000 with a corresponding call accuracy of 99.9%.
Sequencing data quality
| Flow cell type | 5Mb | 25Mb | 50Mc | 100Mc |
|---|---|---|---|---|
| 1 × 100 bp | ≥ 90% of bases higher than Q30 | |||
| 2 × 150 bp | ≥ 90% of bases higher than Q30 | |||
| 2 x 300 bp | ≥ 85% of bases higher than Q30 | |||
a. The percentage of bases ≥ Q30 is averaged across the entire sequencing run. Quality scores are based on MiSeq i100 Series reagents using an Illumina PhiX control library.
b. 5M and 25M flow cells available now.
c. 50M and 100M flow cells will be available starting in 2025 for the MiSeq i100 Plus System only.
Run time
What is run time? Sequencing run time includes cluster generation, onboard denaturation, sequencing, base calling, and quality scoring on the instrument.
| Flow cell type | 5Ma | 25Ma | 50Mb | 100Mb |
|---|---|---|---|---|
| 1 × 100 bp | — | ~ 4 hr | ~ 4.5 hr | ~ 5 hr |
| 2 × 150 bp | ~ 7 hr | ~ 7 hr | ~ 7.5 hr | ~ 8 hr |
| 2 x 300 bp | ~ 15 hr | ~ 15 hr | ~ 15.5 hr | — |
a. 5M and 25M flow cells available now.
b. 50M and 100M flow cells will be available starting in 2025 for the MiSeq i100 Plus System only.
Estimated sample throughput for key applicationsa
What is sample throughput? Sample throughput is the number of samples that can be sequenced in a single run per flow cell.
| Number of samples per flow cell | |||||
| Application | Reads per sample | 5Mb | 25Mb | 50Mc | 100Mc |
| Transcriptomics | |||||
| 3’ gene expression | 1−5M | 1−5 | 5−25 | 10−50 | 25−100 |
| Targeted RNA panel | 1−5M | 1−5 | 5−25 | 10−50 | 25−100 |
| mRNA-Seq | 10−25M | — | 1−2 | 1−5 | 1−10 |
| Total RNA-Seq | 50M | — | — | 1 | 1−2 |
| Microbial genomics | |||||
| Pathogen detection | 0.5−1M | 1−10 | 1−50 | 1−100 | 1−200 |
| 16S amplicon sequencing | 0.1−0.2M | 1−50 | 1−250 | 1−384 | 1−384 |
| Shallow shotgun metagenomics | 0.5−10M | 1−10 | 1−12 | 1−25 | 1−50 |
| Shotgun metagenomics | 10−25M | — | 1−2 | 1−5 | 1−10 |
| Small WGSd | 0.5M | 1−10 | 1−50 | 1−100 | 1−200 |
| Targeted gene sequencing | |||||
| Amplicon-based | 0.1−50M | 1−5 | 1−250 | 1−384 | 1−384 |
| Enrichment-based | 0.1−50M | 1−50 | 1−250 | 1−384 | 1−384 |
| Genome editing | 0.1−50M | 1−50 | 1−250 | 1−384 | 1−384 |
| Immune repertoire | 2−25M | — | 1−12 | 1−25 | 1-50 |
| Quality control | |||||
| Library QC | > 0.02M | up to 384-plex | up to 384-plex | up to 384-plex | |
a. Reads per sample and sample throughputs are estimates and highly variable, depending on the panel and desired coverage.
b. 5M and 25M flow cells available now.
c. 50M and 100M flow cells will be available starting in 2025 for the MiSeq i100 Plus System only.
d. Estimated reads per sample based on minimum 30× coverage of an average 5MB bacterial genome.
Instrument specifications
MiSeq i100 Series specificationsa
-
Output rangeb1.5–30 Gb
-
Paired-end reads per run10–200M
-
Max read length2 x 300 bp
-
Run time~4–15.5 hr
a. Specifications based on Illumina PhiX control library at supported cluster densities.
b. Maximum range based on 100M flow cell specifications. The 100M flow cell will be available starting in 2025 for the MiSeq i100 Plus System only.
Key technologies
The reagents are shipped and stored at room temperature and ready to use immediately, expediting sequencing setup.
XLEAP-SBS chemistry is our fastest, most robust, highest-quality sequencing chemistry to date.
Flow cells and fluidics integrated in a single cartridge simplify setup and eliminate washes.
Predesigned DRAGEN pipelines onboard the MiSeq i100 Series and in the cloud streamline data analysis.