Table 2.
High Throughput Sequencing Platforms; Applications, Strengths and Weaknesses
| Platform | Advantages | Disadvantages | Applications |
|---|---|---|---|
| Roche | |||
| GS Junior System | Short run time, long reads | Low sequencing depth | Amplicon |
| GS FLX+ System | Sequence Capture | ||
| Whole Genome | |||
| Metagenomics | |||
| Transcriptome | |||
| Illumina | |||
| MISEQ | high throughput | DNA sequence amplification bias | De novo genomes, transcriptomes, metagenomes |
| Illumina HiSeq2500 | |||
| Dual Flow Cell | |||
| HIGH OUTPUT RUN MODE | Ultra-high throughput (Up to 3 billion single reads or 6 billion paired-end reads) | Amplification bias | De novo genomes, transcriptomes, metagenomes |
| RAPID RUN MODE | Ultra-high throughput Up to 600 million single reads or 1.2 billion paired-end reads | Amplification bias | De novo genomes, transcriptomes, metagenomes |
| ABI SOLiD | |||
| 5500xl System | Ultra-high throughput | Amplification bias | De novo genomes, transcriptomes, metagenomes |
| Ion Torrent | |||
| Ion PGM | high throughput | Amplification bias | Targeted sequencing, Copy number analysis, de novo small genome sequencing, |
| Metagenomics, ChIP sequencing, Methylation analysis | |||
| Ion Proton | high throughput (60–80 million reads passing filter) | Amplification bias | Genome, Exome, Gene, ChIP, Methylation, Transcriptome sequencing |
| Pacific Biosciences PacBio RS | Long read sequencing | Low single pass accuracy ~85% | Small Genome Sequencing, Targeted Sequencing, DNA Base Modification Analysis |