Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing.
作者： David E. Cook , Jose Espejo Valle-Inclan , Alice Pajoro , Hanna Rovenich , Bart P.H.J. Thomma
DOI: 10.1104/PP.18.00848
关键词:
摘要: Single-molecule full-length complementary DNA (cDNA) sequencing can aid genome annotation by revealing transcript structure and alternative splice forms, yet current pipelines do not incorporate such information. Here we present long-read (LoReAn) software, an automated pipeline utilizing short- cDNA sequencing, protein evidence, ab initio prediction to generate accurate annotations. Based on annotations of two fungal genomes (Verticillium dahliae Plicaturopsis crispa) plant (Arabidopsis [Arabidopsis thaliana] Oryza sativa), show that LoReAn outperforms popular integrating single-molecule cDNA-sequencing data generated from either the Pacific Biosciences or MinION platforms, correctly predicting gene structure, capturing genes missed other pipelines.
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