Chlomito: a novel tool for precise elimination of organelle genome contamination from nuclear genome assembly.

ABSTRACT:

Introduction

Accurate reference genomes are fundamental to understanding biological evolution, biodiversity, hereditary phenomena and diseases. However, many assembled nuclear chromosomes are often contaminated by organelle genomes, which will mislead bioinformatic analysis, and genomic and transcriptomic data interpretation.

Methods

To address this issue, we developed a tool named Chlomito, aiming at precise identification and elimination of organelle genome contamination from nuclear genome assembly. Compared to conventional approaches, Chlomito utilized new metrics, alignment length coverage ratio (ALCR) and sequencing depth ratio (SDR), thereby effectively distinguishing true organelle genome sequences from those transferred into nuclear genomes via horizontal gene trans

SUBMITTER: Song W 

PROVIDER: S-EPMC11385003 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature