Illumina Microbial Amplicon Prep

A flexible and streamlined NGS library prep kit that enables various public health surveillance and microbial research applications.

< 9 hr

Assay time

~3 hr for 48 samples

Hands-on time

Varies depending on sample source

Input quantity

See full details in the specifications table


Illumina Microbial Amplicon Prep (iMAP) is an amplicon-based library preparation kit built on the same chemistry as COVIDSeq. Library preparation is fast and simple, with libraries compatible with nearly all Illumina sequencing systems. It can be used for various infectious disease, public health surveillance, and microbial research applications, including viral whole-genome sequencing, antimicrobial resistance marker analysis, bacterial and fungal identification, and more.

Expand your microbial research capabilities

Get sequencing results with exceptional data quality and accuracy at any scale with low hands-on time.

  • Target variants with ready-to-use or lab-designed oligos

  • Use a multiplexed, PCR-based workflow

  • Interpret data with simple analysis solutions

  • Sequence a broad range of samples

The kit can be used with custom, published, or commercially available primer sets (primer oligos are not included) and is compatible with RNA or DNA extracted from sources such as cultures, swabs (nasopharyngeal, skin, and nasal), wastewater, and more. Analysis can be performed using the DRAGEN Targeted Microbial App on Basespace Sequence Hub with pre-loaded targets. Files can also be easily uploaded for custom analyses.

Illumina tested protocols
  • Chikungunya1
  • Dengue1
  • Mpox1
  • RSV1
  • Zika1

*Protocols provided for informational purposes only. This does not imply the protocols are validated or supported by Illumina.



1. Illumina. Accessed September 8, 2023, from Illumina Microbial Amplicon Prep for viral surveillance

2. DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus V.2. Accessed September 8, 2023, from

3. Bhatt L, Bhoyar RC, Jolly B, Israni R, Vignesh H, Scaria V, Sivasubbu S. The genome sequence of lumpy skin disease virus from an outbreak in India suggests a distinct lineage of the virus. Arch Virol. 2023 Feb 5;168(3):81. doi: 10.1007/s00705-023-05705-w.

4. Monkeypox virus multiplexed PCR amplicon sequencing (PrimalSeq) V.4. Accessed September 8, 2023, from

5. Whole-Genome Amplification of Respiratory Syncytial Virus (RSV) using Illumina CovidSeq reagents for Next-Generation Sequencing V.2. Accessed September 8, 2023, from

6. SARS-CoV-2 version 5.3.2 scheme release. Accessed September 12, 2023, from

7. Rabies Virus Bat-Clade Sequencing. Accessed October 30, 2023, from



Example workflow

Related applications and methods

Illumina Microbial Amplicon Prep


48-sample amplicon kit containing cDNA conversion, library prep, and indexes. Primers are not included.

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