ntEdit

"ntEdit" is a Bloom filter-based genome sequence editing utility that addresses the challenges of correcting base errors in genome sequence assemblies. Recognizing the limitations of existing polishing utilities that require high read coverage and struggle with scalability, ntEdit offers a robust solution that efficiently scales to large genomes, including those of mammals and conifers.

Key Features and Functionalities:

- Efficient Base Error Correction: ntEdit is capable of fixing the majority (>97%) of base substitutions and indels, even at low sequence depths (<20×), providing a high level of accuracy in genome assembly improvement.

- Scalability to Large Genomes: Unlike many other polishing utilities, ntEdit scales well to large genomes, making it suitable for a wide range of genomic projects from bacteria to conifers and mammals.

- Consistent Performance Across Coverage Levels: Its performance remains constant regardless of increased coverage, ensuring reliable base correction across various sequencing depths.

- Rapid Execution: ntEdit is designed for efficiency, with the ability to execute in less than 14 seconds and less than 3 minutes on average for E. coli and C. elegans genomes, respectively, using a single CPU.