Team I Genome Assembly Group: Difference between revisions

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=== Our Goals ===
=== Our Goals ===
1. To perform quality control on reads before and after assembling the genome.
1. To perform quality control on reads before and after assembling the genome.
2. To evaluate the performance of assembly tools:
2. To evaluate the performance of assembly tools:
   * Abyss
   * Abyss
Line 25: Line 26:
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler, QUAST: quality assessment tool for genome assemblies, Bioinformatics, Volume 29, Issue 8,
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler, QUAST: quality assessment tool for genome assemblies, Bioinformatics, Volume 29, Issue 8,
15 April 2013, Pages 1072–1075, https://doi.org/10.1093/bioinformatics/btt086
15 April 2013, Pages 1072–1075, https://doi.org/10.1093/bioinformatics/btt086
Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol.
Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol.
2012;19(5):455–477. doi:10.1089/cmb.2012.0021
2012;19(5):455–477. doi:10.1089/cmb.2012.0021
Butler, Jonathan et al. “ALLPATHS: de novo assembly of whole-genome shotgun microreads.” Genome research vol. 18,5 (2008): 810-20.
Butler, Jonathan et al. “ALLPATHS: de novo assembly of whole-genome shotgun microreads.” Genome research vol. 18,5 (2008): 810-20.
doi:10.1101/gr.7337908
doi:10.1101/gr.7337908
Earl, Dent et al. “Assemblathon 1: a competitive assessment of de novo short read assembly methods.” Genome research vol. 21,12 (2011): 2224-41.
Earl, Dent et al. “Assemblathon 1: a competitive assessment of de novo short read assembly methods.” Genome research vol. 21,12 (2011): 2224-41.
doi:10.1101/gr.126599.111
doi:10.1101/gr.126599.111
Maccallum, Iain et al. “ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.” Genome biology vol. 10,10 (2009):
Maccallum, Iain et al. “ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.” Genome biology vol. 10,10 (2009):
R103. doi:10.1186/gb-2009-10-10-r103
R103. doi:10.1186/gb-2009-10-10-r103
Miller, Jason R et al. “Assembly algorithms for next-generation sequencing data.” Genomics vol. 95,6 (2010): 315-27. doi:10.1016/j.ygeno.2010.03.001
Miller, Jason R et al. “Assembly algorithms for next-generation sequencing data.” Genomics vol. 95,6 (2010): 315-27. doi:10.1016/j.ygeno.2010.03.001
Pritt, J., Chen, N. & Langmead, B. FORGe: prioritizing variants for graph genomes. Genome Biol 19, 220 (2018). https://doi.org/10.1186/s13059-018-1595-x
Pritt, J., Chen, N. & Langmead, B. FORGe: prioritizing variants for graph genomes. Genome Biol 19, 220 (2018). https://doi.org/10.1186/s13059-018-1595-x
Quainoo, S., Coolen, J.P., Hijum, S.A., Huynen, M.A., Melchers, W.J., Schaik, W.V., & Wertheim, H.F. (2017). Whole-Genome Sequencing of Bacterial Pathogens:
Quainoo, S., Coolen, J.P., Hijum, S.A., Huynen, M.A., Melchers, W.J., Schaik, W.V., & Wertheim, H.F. (2017). Whole-Genome Sequencing of Bacterial Pathogens:
the Future of Nosocomial Outbreak Analysis. Clinical microbiology reviews, 30 4, 1015-1063 .
the Future of Nosocomial Outbreak Analysis. Clinical microbiology reviews, 30 4, 1015-1063 .
Rahman, A., Pachter, L. CGAL: computing genome assembly likelihoods. Genome Biol 14, R8 (2013). https://doi.org/10.1186/gb-2013-14-1-r8
Rahman, A., Pachter, L. CGAL: computing genome assembly likelihoods. Genome Biol 14, R8 (2013). https://doi.org/10.1186/gb-2013-14-1-r8
Salzberg, Steven L et al. “GAGE: A critical evaluation of genome assemblies and assembly algorithms.” Genome research vol. 22,3 (2012): 557-67.
Salzberg, Steven L et al. “GAGE: A critical evaluation of genome assemblies and assembly algorithms.” Genome research vol. 22,3 (2012): 557-67.
doi:10.1101/gr.131383.111
doi:10.1101/gr.131383.111
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages
i884–i890, https://doi.org/10.1093/bioinformatics/bty560
i884–i890, https://doi.org/10.1093/bioinformatics/bty560
Sohn, Jang-il; Nam, Jin-Wu. “The present and future of de novo whole-genome assembly”, Briefings in Bioinformatics, Vol 19.1 (2018).
Sohn, Jang-il; Nam, Jin-Wu. “The present and future of de novo whole-genome assembly”, Briefings in Bioinformatics, Vol 19.1 (2018).
doi.org/10.1093/bib/bbw096
doi.org/10.1093/bib/bbw096
Souvorov A., Agarwala R., & Lipman D.J. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biology. 2018; 19(1).
Souvorov A., Agarwala R., & Lipman D.J. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biology. 2018; 19(1).
doi:10.1186/s13059-018-1540-z
doi:10.1186/s13059-018-1540-z
Tanja Magoc, Stephan Pabinger, Stefan Canzar, Xinyue Liu, Qi Su, Daniela Puiu, Luke J. Tallon, Steven L. Salzberg, GAGE-B: an evaluation of genome assemblers
Tanja Magoc, Stephan Pabinger, Stefan Canzar, Xinyue Liu, Qi Su, Daniela Puiu, Luke J. Tallon, Steven L. Salzberg, GAGE-B: an evaluation of genome assemblers
for bacterial organisms, Bioinformatics, Volume 29, Issue 14, 15 July 2013, Pages 1718–1725, https://doi.org/10.1093/bioinformatics/btt273
for bacterial organisms, Bioinformatics, Volume 29, Issue 14, 15 July 2013, Pages 1718–1725, https://doi.org/10.1093/bioinformatics/btt273
Zerbino, D., & Birney, E. (n.d.). Velvet: de novo assembly using very short reads. Hinxton: European Bioinformatics Institute.
Zerbino, D., & Birney, E. (n.d.). Velvet: de novo assembly using very short reads. Hinxton: European Bioinformatics Institute.

Revision as of 17:53, 29 January 2020

Team 1 Genome Assembly

In-Class Presentations

File:Team 1 Genome Assembly Presentation 1.pdf

Genome Assembly Pipeline

Our Goals

1. To perform quality control on reads before and after assembling the genome.

2. To evaluate the performance of assembly tools: 

  * Abyss
  * ALLPATHS-LG
  * SPADES
  * SKESA
  * Velvet

3. To use the best 2 to perform de novo assembly based on the 50 isolates.

4. To send off the highest quality result to gene prediction.


References

Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler, QUAST: quality assessment tool for genome assemblies, Bioinformatics, Volume 29, Issue 8, 15 April 2013, Pages 1072–1075, https://doi.org/10.1093/bioinformatics/btt086

Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–477. doi:10.1089/cmb.2012.0021

Butler, Jonathan et al. “ALLPATHS: de novo assembly of whole-genome shotgun microreads.” Genome research vol. 18,5 (2008): 810-20. doi:10.1101/gr.7337908

Earl, Dent et al. “Assemblathon 1: a competitive assessment of de novo short read assembly methods.” Genome research vol. 21,12 (2011): 2224-41. doi:10.1101/gr.126599.111

Maccallum, Iain et al. “ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.” Genome biology vol. 10,10 (2009): R103. doi:10.1186/gb-2009-10-10-r103

Miller, Jason R et al. “Assembly algorithms for next-generation sequencing data.” Genomics vol. 95,6 (2010): 315-27. doi:10.1016/j.ygeno.2010.03.001

Pritt, J., Chen, N. & Langmead, B. FORGe: prioritizing variants for graph genomes. Genome Biol 19, 220 (2018). https://doi.org/10.1186/s13059-018-1595-x

Quainoo, S., Coolen, J.P., Hijum, S.A., Huynen, M.A., Melchers, W.J., Schaik, W.V., & Wertheim, H.F. (2017). Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clinical microbiology reviews, 30 4, 1015-1063 .

Rahman, A., Pachter, L. CGAL: computing genome assembly likelihoods. Genome Biol 14, R8 (2013). https://doi.org/10.1186/gb-2013-14-1-r8

Salzberg, Steven L et al. “GAGE: A critical evaluation of genome assemblies and assembly algorithms.” Genome research vol. 22,3 (2012): 557-67. doi:10.1101/gr.131383.111

Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560

Sohn, Jang-il; Nam, Jin-Wu. “The present and future of de novo whole-genome assembly”, Briefings in Bioinformatics, Vol 19.1 (2018). doi.org/10.1093/bib/bbw096

Souvorov A., Agarwala R., & Lipman D.J. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biology. 2018; 19(1). doi:10.1186/s13059-018-1540-z

Tanja Magoc, Stephan Pabinger, Stefan Canzar, Xinyue Liu, Qi Su, Daniela Puiu, Luke J. Tallon, Steven L. Salzberg, GAGE-B: an evaluation of genome assemblers for bacterial organisms, Bioinformatics, Volume 29, Issue 14, 15 July 2013, Pages 1718–1725, https://doi.org/10.1093/bioinformatics/btt273

Zerbino, D., & Birney, E. (n.d.). Velvet: de novo assembly using very short reads. Hinxton: European Bioinformatics Institute.

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