ArticleBMC genomics2013
Assessing De Novo transcriptome assembly metrics for consistency and utility.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 1 of them a synthesis that pooled it.
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Who cites it
60 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- De Novo transcriptome assembly of Diaprepes abbreviatus: foundations for functional genomics and targeted pest management.BMC genomics · 2025Article
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- De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide.Frontiers in zoology · 2024Review
- Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets.Bioinformatics and biology insights · 2024Article
- Elucidating the Mesocarp Drupe Transcriptome of Açai (International journal of molecular sciences · 2023Article
- Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study inPlants (Basel, Switzerland) · 2022Article
- Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae).BMC genomics · 2022Article
- SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Frontiers in genetics · 2022Article
- CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.PLoS computational biology · 2021Article
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- Transcriptome Landscape Variation in the GenusGenes · 2019Article
- De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing.Scientific reports · 2019Article
- Transcriptome, proteome and draft genome of Euglena gracilis.BMC biology · 2019Article
- Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Revisiting avian 'missing' genes from de novo assembled transcripts.BMC genomics · 2019Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundTranscriptome 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.
resultsWe 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.
conclusionsAlthough 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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