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MiSeq (Illumina) sequencing

Capabilities

With its ability to produce long paired-end reads (up to 2 x 300 bp), the Illumina MiSeq instrument is ideal for de novo assembly of small genomes or amplicon sequencing projects.

  • Runs may be configured with some flexibility (e.g. a 50 bp kit can be used for a paired-end 2 x 25 bp run).
  • MiSeq have a single lane per flowcell. These instruments can rapidly run a single sample or pool of samples. Currently, the maximum read length isĀ 300 bp. Depending on the application, the run time ranges from 1 to 2 days.
  • The run time and output per flowcell vary depending on the application, as indicated in the tables below.
MiSeq v2 kits Run time Reads passing filter (M/lane) Pass filter output (Gbp/run)
50 bp kit (single-end 50bp) ~1 day 12-15 0.6-0.75
300 bp kit (paired-end 2 x 150 bp) ~1.5 day 24-30 3.6-4.5
500 bp kit (paired-end 2 x 250 bp) ~2 days 24-30 7.2-9
MiSeq v3 kits Run time Reads passing filter (M/lane) Pass filter output (Gbp/run)
150 bp kit (single-end 150bp) ~1.5 day 22-25 3.3-3.75
150 bp kit (paired-end 2 x 75 bp) ~1.5 day 44-50 3.3-3.75
600 bp kit (paired-end 2 x 300 bp) ~3 days 44-50 13-15
MiSeq v2 kits Run time Reads passing filter (M/lane) Pass filter output (Gbp/run)
300 bp kit (paired-end 2 x 150 bp) inquire 2 0.3
500 bp kit (paired-end 2 x 350 bp) inquire 2 0.5
MiSeq Micro kits Run time Reads passing filter (M/lane) Pass filter output (Gbp/run)
300 bp kit (paired-end 2 x 150 bp) inquire 8 1.2

Flexibility

We provide a variety of read length options, as reflected in our price list. With the MiSeq instrument, runs can be configured with some flexibility. For example, a 50 bp kit can be used for a paired-end 2 x 25 bp run. In some cases, we may be able to offer custom read lengths. Please contact us to discuss options for your project.

Don't overpay for bad samples

When you place an order for sequencing of a library that you prepared with our Illumina Library small project pipeline, we automatically include an internal QC before sequencing your samples. If the QC results are very poor and sequencing is not recommended, we will not process your samples. You will be charged only for the QC, not the sequencing of samples that are likely to fail.

Service pricing

MiSeq (Illumina) sequencing
DescriptionInternal price (Cornell and Cornell affiliates)External price
50 bp sequencing kit (v2)* $992 $1,627
300 bp sequencing kit (v2)* (e.g. 2 x 150 bp) $1,263 $2,071
500 bp sequencing kit (v2)* (e.g. 2 x 250 bp) $1,422 $2,333
150 bp sequencing kit (v3)* (e.g. 2 x 75 bp) $1,090 $1,788
600 bp sequencing kit (v3)* (e.g. 2 x 300 bp) $1,818 $2,982
300 bp Nano kit**, ~1 M clusters sequenced $321 $527
500 bp Nano kit, ~1 M clusters sequenced $385 $631
300 bp Micro kit, ~4 M clusters sequenced $482 $790
* Nominal read lengths--different length runs can be performed, depending on the type of sample/indexing used.
** Smaller output kits, usually not kept in stock.