Skip to main content
SpringerLink
Log in

A Domain Framework Approach for Quality Feature Analysis of Genome Assemblies

  • Conference paper
  • First Online:
Advances in Bioinformatics and Computational Biology (BSB 2019)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 11347))

Included in the following conference series:

Abstract

The Genome Assembly research area has quickly evolved, adapting to new sequencing technologies and modern computational environments. There exist many assembler software systems that consider multiple approaches; however, at the end of the process, the assembly quality can always be questioned. When an assembly is accomplished, one may generate quality features for its qualification. Nonetheless, these features do not directly explain the assembly quality; instead, they only list quantitative assembly descriptions. This work proposes GAAF (Genome Assembly Analysis Framework), a domain framework for the feature analysis post-genome Assembly process. GAAF works with distinct species, assemblers, and features, and its goal is to enable data interpretation and assembly quality evaluation.

GitHub: https://github.com/neumannguib/GAAF-Framework.

Supported by National Council for the Improvement of Higher Education (CAPES).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    A Feature is a measurable property or characteristic that describes an object or phenomenon under observation [3].

References

  1. Bradnam, K.R., et al.: Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2(1), 2047–217X (2013). https://doi.org/10.1186/2047-217X-2-10

    Article  Google Scholar 

  2. Castro, C.J., Ng, T.F.F.: U50: a new metric for measuring assembly output based on non-overlapping target-specific contigs. J. Comput. Biol. 24(11), 1071–1080 (2017). https://doi.org/10.1089/cmb.2017.0013

    Article  MathSciNet  Google Scholar 

  3. Bishop, C.M.: Pattern Recognition and Machine Learning. Springer, New York (2006)

    MATH  Google Scholar 

  4. Darling, A.E., Tritt, A., Eisen, J.A., Facciotti, M.T.: Mauve assembly metrics. Bioinformatics 27(19), 2756–2757 (2011). https://doi.org/10.1093/bioinformatics/btr451

    Article  Google Scholar 

  5. Denton, J.F., Lugo-Martinez, J., Tucker, A.E., Schrider, D.R., Warren, W.C., Hahn, M.W.: Extensive error in the number of genes inferred from draft genome assemblies. PLoS Comput. Biol. 10(12), e1003998 (2014). https://doi.org/10.1371/journal.pcbi.1003998

    Article  Google Scholar 

  6. Fayad, M., Schmidt, D.: Object-oriented application frameworks naval open systems architecture strategy view project unified software engines (USEs): a unified approach to building software systems View project. Commun. ACM (1997). https://doi.org/10.1145/262793.262798

    Article  Google Scholar 

  7. Gurevich, A., Saveliev, V., Vyahhi, N., Tesler, G.: QUAST : quality assessment tool for genome assemblies. Bioinformatics 29(8), 1072–1075 (2013). https://doi.org/10.1093/bioinformatics/btt086

    Article  Google Scholar 

  8. Hu, X., et al.: pIRS: Profile-based Illumina pair-end reads simulator. Bioinformatics 28(11), 1533–1535 (2012). https://doi.org/10.1093/bioinformatics/bts187

    Article  Google Scholar 

  9. Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M., Otto, T.D.: REAPR: a universal tool for genome assembly evaluation. Genome Biol. 14(5), R47 (2013). https://doi.org/10.1186/gb-2013-14-5-r47

    Article  Google Scholar 

  10. Land, M.L., et al.: Quality scores for 32,000 genomes. Stan. Genomic Sci. 9(1), 20 (2014). https://doi.org/10.1186/1944-3277-9-20

    Article  Google Scholar 

  11. Landin, N., Niklasson, A., Regnell, B.: Development of Object-Oriented Frameworks (1995)

    Google Scholar 

  12. Liu, D., Hunt, M., Tsai, I.J.: Inferring synteny between genome assemblies: a systematic evaluation. BMC Bioinform. 19(1), 1–6 (2018). https://doi.org/10.1186/s12859-018-2026-4

    Article  Google Scholar 

  13. Magoc, T., et al.: GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics (Oxford, England) 29(14), 1718–1725 (2013). https://doi.org/10.1093/bioinformatics/btt273

    Article  Google Scholar 

  14. Vezzi, F., Narzisi, G., Mishra, B.: Feature-by-feature - evaluating de novo sequence assembly. PLoS ONE 7(2), e31002 (2012). https://doi.org/10.1371/journal.pone.0031002

    Article  Google Scholar 

  15. Vezzi, F., Narzisi, G., Mishra, B.: Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons. PLoS ONE 7(12), e52210 (2012). https://doi.org/10.1371/journal.pone.0052210

    Article  Google Scholar 

  16. Waterhouse, R.M., et al.: BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol. Biol. Evol. 35(3), 543–548 (2017). https://doi.org/10.1093/molbev/msx319

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rio de Janeiro, Brazil

    Guilherme Borba Neumann, Elvismary Molina de Armas, Fernanda Araujo Baiao, Ruy Luiz Milidiu & Sergio Lifschitz

Authors
  1. Guilherme Borba Neumann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Elvismary Molina de Armas
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fernanda Araujo Baiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ruy Luiz Milidiu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sergio Lifschitz
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Guilherme Borba Neumann .

Editor information

Editors and Affiliations

  1. Fluminense Federal University, Niterói, Brazil

    Luis Kowada

  2. Fluminense Federal University, Niterói, Brazil

    Daniel de Oliveira

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Neumann, G.B., de Armas, E.M., Baiao, F.A., Milidiu, R.L., Lifschitz, S. (2020). A Domain Framework Approach for Quality Feature Analysis of Genome Assemblies. In: Kowada, L., de Oliveira, D. (eds) Advances in Bioinformatics and Computational Biology. BSB 2019. Lecture Notes in Computer Science(), vol 11347. Springer, Cham. https://doi.org/10.1007/978-3-030-46417-2_11

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-46417-2_11

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-46416-5

  • Online ISBN: 978-3-030-46417-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation