Next Generation Sequencing: Approach for Assessment and enrichment of raw data

  • Jyoti Kant Choudhari Chhattisgarh Swami Vivekananda Technical University, Bhilai (C.G) India
  • Jyotsna Choubey Sub-DIC Bioinformatics, National Institute of Technology Raipur (C.G.) India
  • Ashish Patel Sub-DIC Bioinformatics, National Institute of Technology Raipur (C.G.) India
Keywords: Next Generating Sequencing, Sequence Quality, FASTQ, Galaxy server

Abstract

Next-generation sequencing (NGS) is a non-sanger technique based on high-throughput capacity for determining the exact order of nucleotide in the given DNA & RNA molecule. Modern high-throughput sequencer’s produce millions of sequences read in a single run. The quality of these data are not perfect because they contains artefacts like poor quality reads, adapter contamination, wrong base calls and INDELs due to instrument failure or chemical process error. In this study, a procedure has been designed for the refinement and improvement of quality of NGS data for further biological processes.

References

1. Yang, Yaran, Bingbing Xie, and Jiangwei Yan. "Application of Next-generation Sequencing Technology in Forensic Science." Genomics, proteomics & bioinformatics 12.5 (2014): 190-197.
2. Grada, Ayman, and Kate Weinbrecht. "Next-generation sequencing: methodology and application." Journal of Investigative Dermatology 133, no. 8 (2013): e11.
3. Schuster, Stephan C. "Next-generation sequencing transforms today’s biology."Nature 200, no. 8 (2007): 16-18.
4. Mardis, Elaine R. "Next-generation DNA sequencing methods." Annu. Rev. Genomics Hum. Genet. 9 (2008): 387-402.
5. Egan, A. N., Schlueter, J., & Spooner, D. M. (2012). Applications of next-generation sequencing in plant biology. American Journal of Botany, vol. 99 no. 2 175-185
6. Cock, P. J., Fields, C. J., Goto, N., Heuer, M. L., & Rice, P. M. (2010). The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic acids research, 38(6), 1767-1771.
7. Nagarajan, N., & Pop, M. (2010). Sequencing and genome assembly using next-generation technologies. Computational Biology, 1-17.
8. Gordon, A., & Hannon, G. J. (2010). Fastx-toolkit. FASTQ/A short-reads preprocessing tools (unpublished) http://hannonlab. cshl. edu/fastx_toolkit.
9. Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data.175-176
10. Goecks, J., Nekrutenko, A., & Taylor, J. (2010). Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome biology, 11(8), R86.
11. Schmeier, S. (2017). Genomics Tutorial. (https://sschmeier.com)
12. Blankenberg, D., Gordon, A., Von Kuster, G., Coraor, N., Taylor, J., & Nekrutenko, A. (2010). Manipulation of FASTQ data with Galaxy. Bioinformatics, 26(14), 1783-1785.
13. Gordon, A., & Hannon, G. J. (2010). Fastx-toolkit. FASTQ/A short-reads preprocessing tools (unpublished) http://hannonlab. cshl. edu/fastx_toolkit.
Published
2017-09-14
Section
Articles