ntEdit: scalable genome sequence polishing.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Genome sequence assemblies are common but can contain base errors.
• Existing genome polishing tools require high read coverage and do not scale well for large genomes.

Purpose of the Study:

• To develop and evaluate ntEdit, a scalable genome sequence editing utility.
• To address limitations of current tools in handling base errors in large genomes.

Main Methods:

• Developed ntEdit, a Bloom filter-based genome sequence editing utility.
• Benchmarked ntEdit against GATK, Pilon, and Racon using E. coli, C. elegans, and human genome datasets.
• Tested ntEdit on large mammalian and conifer genomes, including spruce.

Main Results:

• ntEdit effectively corrects >97% of base substitutions and indels at low sequence depths (<20×).
• The tool demonstrates consistent performance with increased coverage and scales linearly for large genomes.
• ntEdit processed human genome sequences in 30-40 minutes and large spruce genomes in under 5 hours, making millions of accurate edits.

Conclusions:

• ntEdit is a highly efficient and scalable tool for genome sequence editing.
• It overcomes limitations of existing methods, particularly for large genomes and low-coverage data.
• The utility provides accurate base polishing across diverse species, advancing genomic research.