Safar, H.A.; Alatar, F.; Mustafa, A.S. Three Rounds of Read Correction Significantly Improve Eukaryotic Protein Detection in ONT Reads. Microorganisms2024, 12, 247.
Safar, H.A.; Alatar, F.; Mustafa, A.S. Three Rounds of Read Correction Significantly Improve Eukaryotic Protein Detection in ONT Reads. Microorganisms 2024, 12, 247.
Safar, H.A.; Alatar, F.; Mustafa, A.S. Three Rounds of Read Correction Significantly Improve Eukaryotic Protein Detection in ONT Reads. Microorganisms2024, 12, 247.
Safar, H.A.; Alatar, F.; Mustafa, A.S. Three Rounds of Read Correction Significantly Improve Eukaryotic Protein Detection in ONT Reads. Microorganisms 2024, 12, 247.
Abstract
Background: Eukaryotes whole-genome sequencing is crucial for species identification, gene detection and protein-annotation. Oxford Nanopore sequencing serves as an affordable and rapid platform for sequencing eukaryotes, however the relatively higher error rates require computational and bioinformatic efforts to produce more accurate genome assemblies. Here, we evaluated the effect of read correction tools on eukaryotes genome completeness, gene detection and protein-annotation. Methods: Reads generated by ONT of four eukaryotes, C. albicans, C. gattii, S. cerevisiae, and P. falciparum, were assembled using minimap2 and underwent three rounds of read correction using flye, medaka and racon. The generates consensus FASTA files were compared for total length (bp), genome completeness, gene detection, and protein-annotation by QUAST, BUSCO, BRAKER1 and InterProScan, respectively. Results: genome completeness was dependent on assembly method rather than read correction tool, however, medaka performed better than flye and racon. Racon significantly performed better than flye and medaka in gene detection, while both racon and medaka significantly performed better than flye in protein-annotation. Conclusion: We show that three rounds of read correction significantly affects gene detection and protein-annotation which are dependent on assembly quality in preference to assembly completeness.
Keywords
Eukaryotes; ONT; read correction; gene detection; protein annotation
Subject
Medicine and Pharmacology, Medicine and Pharmacology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
