The three “bigs” (in no particular order), with some links, basic information collected from the linked websites** and my (subjective) one sentence summary:

Illumina

• Company website

• Technology videos:

• HiSeq 2000 (shows the workflow)

• Animation

• Reads:

  • Read length: 25, 36, 50, 100, 150, 250, read length is uniform (all reads have the same length)

  • Single and paired reads

  • Typical errors: generally high quality

  • Throughput: 540 Mb – 600 Gb

  • Runtime: 4 hours – 11 days

  • Cost: MiSeq – $125,000 (US list price in 2012)**

• Summary: relatively short reads (but they can be paired), relatively slow, high throughput, high quality, high price.

• Additional resources:

  • Does Illumina have a homopolymer error problem as well?

Ion Torrent

• Company website

• You can also take a look at the Ion Torrent subpage on the Life Technologies site here.

• Technology videos:

  • Introduction

• Reads:

  • Read length: around 35 or 200 or 400 bps

  • Single reads (paired end reads have been introduced in 2012, but are still not commercially available).

  • Typical errors:

    • high amount of homoploymer errors

    • lower quality than 454 or Illumina

    • even lower quality at read ends

  • Throughput: from 3 Mb to 1.5 Gb (up to 10 Gb for Ion Proton), depending on read length and the chip used (for details see here).

  • Runtime: 0.5 – 7.3 hours

  • Cost: Ion Torrent PGM – $80,490 (US list price in 2012)**

• Summary: long reads, high-throughput, fast, relatively cheap, but loads of homopolymer errors (over 1%) and lower quality in general.

• Additional resources:

  • About IonTorrent in the Broad Institute (13:45)

Roche 454

• Company website

• Technology videos:

  • Introduction

  • Much better visual representation, but less talk

• Reads:

  • Read length: varies within a same run, the mean read length, depending on the instrument, is around 400-500 or 600-700 bps (theoretically read length can go up to ~1000 bp for GS FLX ).

  • Single and paired end reads

  • Typical errors:

    • homopolymer errors (lower percentage than in IonTorrent) (for details see here).

    • lower quality at read ends

  • Throughput: from 35 Mb (GS Junior) to 700 Mb (GS FLX Titanium XL )

  • Runtime: 10-23 hours

  • Cost: 454 GS Junior – $108,000 (US list price in 2012)**

• Summary: longest reads, good quality, but low throughput and expensive, plus homopolymer errors are typical.

• Additional resources:

  • Accuracy and quality of massively parallel DNA pyrosequencing.

Honorable mentions:

• PacBio

• NanoPore

• Helicos

* Of course, a great amount of development, improvement and testing can be done by “in-company” teams, but in my opinion a substantial user base is crucial for proper, unbiased validation and testing of these sequencing tools.

** Prices were collected from the following article:

Liu et al., (2012) Comparison of Next-Generation Sequencing Systems Journal of Biomedicine and Biotechnology, Volume 2012, Article ID 251364, 11 pages, doi:10.1155/2012/251364, http://www.hindawi.com/journals/bmri/2012/251364/

Special thanks to Tibor Nagy for collecting the videos!