Significantly improving the quality of genome assemblies through curation

By Kerstin Howe, W. Chow, Joanna C. Collins, S. Pelan, Damon-Lee B Pointon, Y. Sims, James H. Torrance, A. Tracey, Jonathan M. D. Wood. bioRxiv, 2020

314 citations recorded by the source corpus.

Background Genome sequence assemblies provide the basis for our understanding of biology. Generating error-free assemblies is therefore the ultimate, but sadly still unachieved goal of a multitude of research projects. Despite the ever-advancing improvements in data generation, assembly algorithms and pipelines, no automated approach has so far reliably generated near error-free genome assemblies for eukaryotes. Results Whilst working towards improved data sets and fully automated pipelines, assembly evaluation and curation is actively employed to bridge this shortcoming and significantly reduce the number of assembly errors. In addition to this increase in product value, the insights gained from assembly curation are fed back into the automated assembly strategy and contribute to notable improvements in genome assembly quality. Conclusions We describe our tried and tested approach for assembly curation using gEVAL, the genome evaluation browser. We outline the procedures applied to genome curation using gEVAL and also our recommendations for assembly curation in an gEVAL-independent context to facilitate the uptake of genome curation in the wider community.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3764b09b9607ebd5d985e407b3f2a5e5a997def2

Citations in the corpus

• Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing (2022, unknown): “However, because genome maps are noisy and scaffolding methods are fallible, automated scaffolding usually results in incomplete or misassembled scaffolds and researchers often rely on laborious manual curation to correct these shortcomings [14, 15].”