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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
Published on: May 9, 2017
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The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly
1Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
Peerj
|August 8, 2018
Summary
The Oyster River Protocol (ORP) offers a standardized method for de novo transcriptome assembly in non-model organisms. This bioinformatics approach improves transcript assembly quality and enhances downstream genomic analyses.
Area of Science:
- Genomics
- Bioinformatics
- Transcriptomics
Background:
- High-throughput sequencing enables extensive studies in functional, evolutionary, and population genomics.
- De novo transcriptome assembly is a crucial but complex initial step for many genomic studies.
Purpose of the Study:
- To introduce and validate the Oyster River Protocol (ORP) for standardized de novo transcriptome assembly.
- To demonstrate ORP's ability to produce higher quality assemblies compared to existing methods.
Main Methods:
- ORP utilizes a multi-assembler and kmer approach to overcome individual assembler limitations.
- The protocol involves a standardized and benchmarked set of bioinformatic processes.
Main Results:
- ORP assemblies exhibit superior Detonate and TransRate scores and higher mapping rates.
- The protocol successfully incorporates previously unassembled transcripts, boosting downstream analysis power.
- Assembly quality is shown to be independent of read count above 30 million.
Conclusions:
- The Oyster River Protocol provides a robust and enhanced method for de novo transcriptome assembly.
- ORP improves the reliability and scope of genomic research in non-model organisms.
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