A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.
- Published: 24 Jul 2012
- Country: United Kingdom
- Cardiff University United Kingdom
- WT - Wellcome Sanger Institute United Kingdom
- Wellcome Trust Sanger Institute
- Funder: Wellcome Trust (WT)
- Project Code: 098051
- Funding stream: Cellular and Molecular Neuroscience
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]
- Cardiff University United Kingdom
- WT - Wellcome Sanger Institute United Kingdom
- Wellcome Trust Sanger Institute
- Funder: Wellcome Trust (WT)
- Project Code: 098051
- Funding stream: Cellular and Molecular Neuroscience
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]