Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in
de novo assembly
hybrid transcriptome
non-model organisms
normalized comparison
optimization
transcriptomics
Journal
Plants (Basel, Switzerland)
ISSN: 2223-7747
Titre abrégé: Plants (Basel)
Pays: Switzerland
ID NLM: 101596181
Informations de publication
Date de publication:
10 Sep 2022
10 Sep 2022
Historique:
received:
23
07
2022
revised:
21
08
2022
accepted:
07
09
2022
entrez:
23
9
2022
pubmed:
24
9
2022
medline:
24
9
2022
Statut:
epublish
Résumé
A high-quality transcriptome is required to advance numerous bioinformatics workflows. Nevertheless, the effectuality of tools for de novo assembly and real precision assembled transcriptomes looks somewhat unexplored, particularly for non-model organisms with complicated (very long, heterozygous, polyploid) genomes. To disclose the performance of various transcriptome assembly programs, this study built 11 single assemblies and analyzed their performance on some significant reference-free and reference-based criteria. As well as to reconfirm the outputs of benchmarks, 55 BLAST were performed and compared using 11 constructed transcriptomes. Concisely, normalized benchmarking demonstrated that Velvet-Oases suffer from the worst results, while the EvidentialGene strategy can provide the most comprehensive and accurate transcriptome of
Identifiants
pubmed: 36145766
pii: plants11182365
doi: 10.3390/plants11182365
pmc: PMC9503428
pii:
doi:
Types de publication
Journal Article
Langues
eng
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