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CGAL: computing genome assembly likelihoods

Rahman, Atif and Pachter, Lior (2013) CGAL: computing genome assembly likelihoods. Genome Biology, 14 (1). Art. No. R8. ISSN 1465-6906. PMCID PMC3663106. doi:10.1186/gb-2013-14-1-r8. https://resolver.caltech.edu/CaltechAUTHORS:20170303-155431520

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Abstract

Assembly algorithms have been extensively benchmarked using simulated data so that results can be compared to ground truth. However, in de novo assembly, only crude metrics such as contig number and size are typically used to evaluate assembly quality. We present CGAL, a novel likelihood-based approach to assembly assessment in the absence of a ground truth. We show that likelihood is more accurate than other metrics currently used for evaluating assemblies, and describe its application to the optimization and comparison of assembly algorithms. Our methods are implemented in software that is freely available at http://bio.math.berkeley.edu/cgal/.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1186/gb-2013-14-1-r8DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663106/PubMed CentralArticle
ORCID:
AuthorORCID
Rahman, Atif0000-0003-1805-3971
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2013 Rahman and Pachter, licensee Springer. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 23 August 2012. Accepted: 29 January 2013. Published: 29 January 2013. We thank Michael Eisen, Aaron Kleinman, Harold Pimentel and Adam Roberts for helpful conversations in the development of the likelihood-based approach for assembly evaluation. LP was funded in part by NIH R21 HG006583. AR was funded in part by Fulbright Science & Technology Fellowship 15093630. Authors' contributions: AR and LP conceived the project and developed the methodology. AR implemented the method in the CGAL software and obtained the results of the paper. AR and LP wrote the manuscript. All authors read and approved the final manuscript. The authors have no competing interests.
Funders:
Funding AgencyGrant Number
NIHR21 HG006583
Fulbright Foundation15093630
Subject Keywords:Genome assembly; evaluation; likelihood; sequencing
Issue or Number:1
PubMed Central ID:PMC3663106
DOI:10.1186/gb-2013-14-1-r8
Record Number:CaltechAUTHORS:20170303-155431520
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170303-155431520
Official Citation:Rahman A, Pachter L. CGAL: computing genome assembly likelihoods. Genome Biology. 2013;14(1):R8. doi:10.1186/gb-2013-14-1-r8.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74740
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:06 Mar 2017 16:45
Last Modified:11 Nov 2021 05:29

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