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Researchers can now have it all—affordability and full flexibility to perform sequencing of small genomes, sets of genes, or transcripts, all on the Ion PGM™ Sequencers. Different sequencing applications have different demands, so we developed two optimized sequencing solutions to meet those needs.

400 base

Long-read, 400-base sequencing enables long-amplicon applications

The Ion PGM™ Sequencing 400 Kit is powered with a new long-read sequencing enzyme and is ideal for:
• De novo sequencing of small genomes (i.e., microbes)
• Targeted sequencing applications including 16S rRNA typing and HLA that benefit from longer reads
• RNA sequencing projects that aim to discover and detect isoforms and novel transcripts

Get better assembly results with four-hour, 400-base sequencing

Comparison of assembly metrics from runs generated using the MiSeq™ Personal Sequencer and the Ion PGM™ Sequencer demonstrate that Ion PGM™ 400-base sequencing outperforms MiSeq sequencer 2 x 250-base sequencing (Table 1) and it does so in only 4 hours of sequencing time for one Ion 314™ Chip (compared to 37 hours on the MiSeq™ Personal Sequencer).

Longer reads. Higher throughput.

Performance results from internal runs demonstrate that the Ion PGM™  Sequencing 400 Kit consistently yields individual reads with long read lengths and high run throughput (Figure 1).

Figure 1.Analysis of internal runs using Ion 318™ Chips and 400-base sequencing. Data was generated using Torrent Suite Software v3.4.

Table 1. Ion PGM™ and MiSeq™ E.coli DH10b assembly data comparison.

*MiSeq™ data was generated, and made publicallly available by Edge BioSystems for 1900x and 30x sequencing coverage. Assembly analysis at 57.59x coverage was performed by Life Technologies using the same method applied to the two Ion PGM™ datasets.
**Dataset available on Ion Community

To get started with 400-base sequencing, use the following:
Ion PGM Template OT2 400 Kit (4479878), compatible with 4482002 and Ion One Touch™ 2 System
Ion PGM™ Sequencing 400 Kit (4482002)
Ion OneTouch™ 2 System (4474779)
Torrent Suite Software v3.4 or higher



200-base sequencing delivers highly accurate detection of low-frequency variants

For targeted gene sequencing applications where accurate variant detection is critical and FFPE samples are often used, we recommend the Ion PGM™ Sequencing Kit 200 v2 in combination with Ion AmpliSeq™ targeted sequencing panels. To obtain the high accuracy results for targeted sequencing, use the latest version of Torrent Suite Software and Ion Reporter Software. This end-to-end product solution delivers primer pools with high design rate and coverage uniformity, optimized sequencing chemistry for high raw accuracy, and analysis software equipped with improved algorithms for both SNP and indel detection.



200-base chemistry reanalyzed with new Torrent Suite Software v3.4 results in higher raw and consensus accuracy

Torrent Suite Software v3.4 incorporates algorithmic improvements in both raw accuracy and consensus variant calling, even in challenging regions such as long homopolymers. These improvements enable the Ion PGM Sequencer to generate data that routinely achieve greater than 99.99% consensus accuracy.

Performance results from 16 internal runs using Ion PGM™ Sequencing Kit 200 v2, reanalyzed with Torrent Suite Software v3.4, demonstrate consistently higher mean raw read accuracy (Table 2) than results with previous software versions. Raw read accuracy is measured at each base across the length of the read and is based on 1x sequencing coverage, not based on consensus accuracy across multiple reads for the same base position.

Table 2. Improved mean raw read accuracy with Ion PGM™ Sequencing Kit 200 v2 data
reanalyzed using Torrent Suite Software v3.4

To get started with 200-base sequencing, use the following:
Ion PGM™ Template OT2 200 Kit (4480974), compatible with 4482006 and Ion One Touch™ 2 System
Ion PGM™ Sequencing 200 Kit v2 (4482006)
Ion One Touch™ 2 System (4474779)
Torrent Suite Software v3.4 or higher


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For research use only. Not for use in diagnostic procedures.