publication . Other literature type . Article . 2012

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.

Michael A. Quail; Simon R. Harris; Miriam Smith; Thomas R. Connor; Thomas D. Otto; Paul Coupland; Anna Bertoni; Yong Gu; Harold Swerdlow;
Open Access
  • Published: 24 Jul 2012
  • Country: United Kingdom
Abstract
<p>Abstract</p> <p>Background</p> <p>Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent’s PGM, Pacific Biosciences’ RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehe...
Subjects
free text keywords: QH301, QH426, Biotechnology, Genetics, Research Article, Next-generation sequencing, Ion torrent, Illumina, MiSeq, PGM, SMRT, Bias, Genome coverage, GC-rich, AT-rich, TP248.13-248.65, QH426-470, GC-content, Pacific biosciences, Context specific, Illumina miseq, DNA sequencing, Genomic library, Genome, Biology, Computational biology, Ion semiconductor sequencing
32 references, page 1 of 3

1. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, et al: An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475(7356):348-352.

2. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, et al: Real-time DNA sequencing from single polymerase molecules. Science 2009, 323(5910):133-138.

3. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al: Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456(7218):53-59. [OpenAIRE]

4. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ: Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G + C)-biased genomes. Nat Methods 2009, 6(4):291-295. [OpenAIRE]

5. Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF, McQuillan JA, Swerdlow HP, Oyola SO: Optimal enzymes for amplifying sequencing libraries. Nat Methods 2011, 9(1):10-11.

6. Syed F, Grunenwald H, Caruccio N: Next-generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition. Nature Methods Application Note 2009, 10:782.

7. Lam HYK, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, et al: Performance comparison of whole-genome sequencing platforms. Nat Biotechnol 2012, 30(1):78-82.

8. Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA: Artemis: An integrated platform for visualisation and analysis of highthroughput sequence-based experimental data. Bioinformatics 2012, 28(4):464-469.

9. Ponsting N, Ning Z: SMALT alignment tool. . (manuscript in preparation). 2012. software download http://www.sanger.ac.uk/resources/software/smalt/.

10. Otto TD, Sanders M, Berriman M, Newbold C: Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 2010, 26(14):1704-1707. [OpenAIRE]

11. Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, et al: Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 2011, 39(13):e90.

12. Diep BA, Gill SR, Chang RF, Phan TH, Chen JH, Davidson MG, Lin F, Lin J, Carleton HA, Mongodin EF, et al: Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet 2006, 367(9512):731-739. [OpenAIRE]

13. Achidi EA, et al: A global network for investigating the genomic epidemiology of malaria. Nature 2008, 456(7223):732-737.

14. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, et al: Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419(6906):498-511.

15. Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloglu A, Ozen S, Sanjad S, et al: Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A 2009, 106(45):19096-19101. [OpenAIRE]

32 references, page 1 of 3
Abstract
<p>Abstract</p> <p>Background</p> <p>Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent’s PGM, Pacific Biosciences’ RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehe...
Subjects
free text keywords: QH301, QH426, Biotechnology, Genetics, Research Article, Next-generation sequencing, Ion torrent, Illumina, MiSeq, PGM, SMRT, Bias, Genome coverage, GC-rich, AT-rich, TP248.13-248.65, QH426-470, GC-content, Pacific biosciences, Context specific, Illumina miseq, DNA sequencing, Genomic library, Genome, Biology, Computational biology, Ion semiconductor sequencing
32 references, page 1 of 3

1. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, et al: An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475(7356):348-352.

2. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, et al: Real-time DNA sequencing from single polymerase molecules. Science 2009, 323(5910):133-138.

3. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al: Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456(7218):53-59. [OpenAIRE]

4. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ: Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G + C)-biased genomes. Nat Methods 2009, 6(4):291-295. [OpenAIRE]

5. Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF, McQuillan JA, Swerdlow HP, Oyola SO: Optimal enzymes for amplifying sequencing libraries. Nat Methods 2011, 9(1):10-11.

6. Syed F, Grunenwald H, Caruccio N: Next-generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition. Nature Methods Application Note 2009, 10:782.

7. Lam HYK, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, et al: Performance comparison of whole-genome sequencing platforms. Nat Biotechnol 2012, 30(1):78-82.

8. Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA: Artemis: An integrated platform for visualisation and analysis of highthroughput sequence-based experimental data. Bioinformatics 2012, 28(4):464-469.

9. Ponsting N, Ning Z: SMALT alignment tool. . (manuscript in preparation). 2012. software download http://www.sanger.ac.uk/resources/software/smalt/.

10. Otto TD, Sanders M, Berriman M, Newbold C: Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 2010, 26(14):1704-1707. [OpenAIRE]

11. Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, et al: Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 2011, 39(13):e90.

12. Diep BA, Gill SR, Chang RF, Phan TH, Chen JH, Davidson MG, Lin F, Lin J, Carleton HA, Mongodin EF, et al: Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet 2006, 367(9512):731-739. [OpenAIRE]

13. Achidi EA, et al: A global network for investigating the genomic epidemiology of malaria. Nature 2008, 456(7223):732-737.

14. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, et al: Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419(6906):498-511.

15. Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloglu A, Ozen S, Sanjad S, et al: Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A 2009, 106(45):19096-19101. [OpenAIRE]

32 references, page 1 of 3
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