Tutorial:Sequencing Technology Review Papers
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Review papers on the topic of sequencing technologies.

  • [Field guide to next-generation DNA sequencers] in Mol Ecol Resour (2011). This paper presents a high level overview of all major and upcoming technologies from the point of view of a sequencing facility manager. It covers the following platforms: 454 (FLX Titanium), Illumina (HiSeq, MiSeq, GA), SOLiD (4, 5500), Helicos, Ion Torrent, PacBio and Starlight. It lists all costs associated with instrument acquisition, library preparation cost per run, cost per sample. Note that the estimates on the sequencing accuracy and computational infrastructure requirements were compiled from vendor supplied information. Edit: the website below publishes yearly updates to the tables in this paper
  • A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers in BMC Genomics (2012). This paper compares various platforms primarily from the perspective of evaluating sequencing accuracy. Three sequencing platforms and various implementation were compared: Illumina (MiSeq, HiSeq, GAII), Ion Torrent PGM and PacBio. Sequencing accuracy tests were performed on genomes with various GC composition from 90%GC to 19% GC content.
  • Performance comparison of benchtop high-throughput sequencing platforms Nature Biotechnology (2012). The authors evaluate the sequencing data produced by three different instruments: 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies). Using data from each instrument they created and compared the de-novo assemblies of a known genome Escherichia coli O104:H4.
  • High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity in Nature Reviews Microbiology (2012). The authors present an overview of high throughput sequencing as it applies to microbiology and bacterial sequencing. Several platforms are enumerated and a high level overview of a typical bacterial sequencing workflow is presented.
  • Performance comparison of whole-genome sequencing platforms in Nature Biotechnology (2012). This paper evaluates data obtained with two sequencing platforms Illumina HiSeq 2000 and Complete Genomics. The authors evaluate the accuracy of sequencing a human genome to a high coverage 76X.
  • Performance comparison of exome DNA sequencing technologies in Nature Biotechnology (2011). This paper presents a comparison of three major commercial exome sequencing platforms from Agilent, Illumina and Nimblegen applied to the same human blood sample.
  • Comparison of Next-Generation Sequencing Systems by BGI. Contains a review based on first-hand extensive experience and discusses the advantages and specifics associated with each sequencing system.

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Tutorial papers sequencing • 17k views
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NextGenSeek ▴ 290

Here is more.

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pengchy ▴ 450

Update to this list from recent years:

Ballester, L.Y., et al. (2016) Advances in clinical next-generation sequencing: target enrichment and sequencing technologies, Expert Rev Mol Diagn, 16, 357-372.

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2194-9

Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148676

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148028

Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling http://aem.asm.org/content/80/24/7583.full

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