Papers by Akriti Bhattarai
ABSTRACTPremise of the studyRobust standards to evaluate quality and completeness are lacking for... more ABSTRACTPremise of the studyRobust standards to evaluate quality and completeness are lacking for eukaryotic structural genome annotation. Genome annotation software is developed with model organisms and does not typically include benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. Plant genomes are particularly challenging with their large genome sizes, abundant transposable elements (TEs), and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and approach on protein-coding gene prediction.MethodsThe impact of repeat masking, long-read, and short-read inputs,de novo, and genome-guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. Annotations were benchmarked for structural traits and sequence similarity.ResultsBenchmarks that reflect gene structures, reciprocal similarity search alignments, and mono-exonic/multi-exonic gene...
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Papers by Akriti Bhattarai