Evaluation of combined genome assemblies

A case study with fungal genomes

Mostafa Abbas, Ponnuraman Balakrishnan, Qutaibah M. Malluhi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The rapid advances in genome sequencing leads to the generation of huge amount of data in a single sequencing experiment. Several genome assemblers with different objectives were developed to process these genomic data. Obviously, the output assemblies produced by these assemblers have different qualities due to their diverse nature. Recent research efforts concluded that combining the assemblies from different assemblers would enhance the quality of the output assembly. Based on this, our study combines the five best assemblies of three fungal genomes and evaluates the quality of the output assembly as compared to that produced by individual assemblers. The results conclude that the output assembly quality is influenced by the increase of the number of gaps in the input assemblies more than the increase in N50 size. Based on this conclusion, we propose a set of guidelines to get better output assemblies.

Original languageEnglish
Title of host publicationBioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings
PublisherSpringer Verlag
Pages333-344
Number of pages12
ISBN (Electronic)9783319164793
Publication statusPublished - 1 Jan 2015
Event3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015 - Granada, Spain
Duration: 15 Apr 201517 Apr 2015

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9044
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015
CountrySpain
CityGranada
Period15/4/1517/4/15

Fingerprint

Genome
Genes
Evaluation
Output
Sequencing
Genomics
Evaluate
Experiment
Experiments

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Abbas, M., Balakrishnan, P., & Malluhi, Q. M. (2015). Evaluation of combined genome assemblies: A case study with fungal genomes. In Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings (pp. 333-344). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9044). Springer Verlag.

Evaluation of combined genome assemblies : A case study with fungal genomes. / Abbas, Mostafa; Balakrishnan, Ponnuraman; Malluhi, Qutaibah M.

Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. Springer Verlag, 2015. p. 333-344 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9044).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abbas, M, Balakrishnan, P & Malluhi, QM 2015, Evaluation of combined genome assemblies: A case study with fungal genomes. in Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9044, Springer Verlag, pp. 333-344, 3rd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, Granada, Spain, 15/4/15.
Abbas M, Balakrishnan P, Malluhi QM. Evaluation of combined genome assemblies: A case study with fungal genomes. In Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. Springer Verlag. 2015. p. 333-344. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
Abbas, Mostafa ; Balakrishnan, Ponnuraman ; Malluhi, Qutaibah M. / Evaluation of combined genome assemblies : A case study with fungal genomes. Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. Springer Verlag, 2015. pp. 333-344 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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