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Assessing De Novo transcriptome assembly metrics for consistency and utility Public Deposited

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  • Background: Transcriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality. Results: We simulated sequencing transcripts of Drosophila melanogaster. By assembling these simulated reads using both a perfect and a modern transcriptome assembler while varying read length and sequencing depth, we evaluated quality metrics to determine whether they 1) revealed perfect assemblies to be of higher quality, and 2) revealed perfect assemblies to be more complete as data quantity increased. Several commonly used metrics were not consistent with these expectations, including average contig coverage and length, though they became consistent when singletons were included in the analysis. We found several annotation-based metrics to be consistent and informative, including contig reciprocal best hit count and contig unique annotation count. Finally, we evaluated a number of novel metrics such as reverse annotation count, contig collapse factor, and the ortholog hit ratio, discovering that each assess assembly quality in unique ways. Conclusions: Although much attention has been given to transcriptome assembly, little research has focused on determining how best to evaluate assemblies, particularly in light of the variety of options available for read length and sequencing depth. Our results provide an important review of these metrics and give researchers tools to produce the highest quality transcriptome assemblies.
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  • O'Neil, S. T., & Emrich, S. J. (2013). Assessing de novo transcriptome assembly metrics for consistency and utility. BMC Genomics, 14(1), 465-465. doi:10.1186/1471-2164-14-465
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  • This work was supported in part by a fellowship to STO as part of the University of Notre Dame’s strategic research investment in global health.
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  • description.provenance : Approved for entry into archive by Deborah Campbell(deborah.campbell@oregonstate.edu) on 2013-09-05T21:50:10Z (GMT) No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) OneilShawnTAssessingDeNovoTranscriptome.pdf: 3704774 bytes, checksum: 9f367bef7d8d813a552cc3bffc9f6005 (MD5)
  • description.provenance : Submitted by Deborah Campbell (deborah.campbell@oregonstate.edu) on 2013-09-05T21:48:34Z No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) OneilShawnTAssessingDeNovoTranscriptome.pdf: 3704774 bytes, checksum: 9f367bef7d8d813a552cc3bffc9f6005 (MD5)
  • description.provenance : Made available in DSpace on 2013-09-05T21:50:10Z (GMT). No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) OneilShawnTAssessingDeNovoTranscriptome.pdf: 3704774 bytes, checksum: 9f367bef7d8d813a552cc3bffc9f6005 (MD5) Previous issue date: 2013-07-09

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