ArticlePeerJ2018
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
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- Gene Expression Shifts in Emperor Penguin Adaptation to the Extreme Antarctic Environment.Molecular ecology · 2025Article
- Phylogenomics reveals the slow-burning fuse of diatom evolution.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Widespread and Convergent Evolution of Cone Monochromacy in Galeomorph Sharks.Molecular biology and evolution · 2025Article
- Light-dependent variations in fatty acid profiles and gene expression in Antarctic microalgal cultures.PloS one · 2025Article
- Semblans: automated assembly and processing of RNA-seq data.Bioinformatics (Oxford, England) · 2024Article
- Egg-laying hormone expression in identified neurons across developmental stages and reproductive states of the nudibranch Berghia stephanieae.Hormones and behavior · 2024Article
- Cellular-resolution gene expression mapping reveals organization in the head ganglia of the gastropod, Berghia stephanieae.The Journal of comparative neurology · 2024Article
- Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring FBMC biology · 2024Article
- Transcriptional Profiling of Early Defense Response to White Pine Blister Rust Infection inGenes · 2024Article
- A genome sequence for the threatened whitebark pine.G3 (Bethesda, Md.) · 2024Article
- Phototactic preference and its genetic basis in the planulae of the colonial HydrozoanbioRxiv : the preprint server for biology · 2024Article
- Article
- Investigating the phylogenetic history of toxin tolerance in mushroom-feedingEcology and evolution · 2023Article
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- Genome assembly of the foot-flagging frog, Staurois parvus: a resource for understanding mechanisms of behavior.G3 (Bethesda, Md.) · 2023Article
- CrusTome: a transcriptome database resource for large-scale analyses across Crustacea.G3 (Bethesda, Md.) · 2023Article
- Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly.BMC bioinformatics · 2023Article
- Latitudinal variation and plasticity in response to temperature inEcology and evolution · 2023Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Characterizing transcriptomes in non-model organisms has resulted in a massive increase in our understanding of biological phenomena. This boon, largely made possible via high-throughput sequencing, means that studies of functional, evolutionary, and population genomics are now being done by hundreds or even thousands of labs around the world. For many, these studies begin with a de novo transcriptome assembly, which is a technically complicated process involving several discrete steps. The Oyster River Protocol (ORP), described here, implements a standardized and benchmarked set of bioinformatic processes, resulting in an assembly with enhanced qualities over other standard assembly methods. Specifically, ORP produced assemblies have higher Detonate and TransRate scores and mapping rates, which is largely a product of the fact that it leverages a multi-assembler and kmer assembly process, thereby bypassing the shortcomings of any one approach. These improvements are important, as previously unassembled transcripts are included in ORP assemblies, resulting in a significant enhancement of the power of downstream analysis. Further, as part of this study, I show that assembly quality is unrelated with the number of reads generated, above 30 million reads. Code Availability: The version controlled open-source code is available at https://github.com/macmanes-lab/Oyster_River_Protocol. Instructions for software installation and use, and other details are available at http://oyster-river-protocol.rtfd.org/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.