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

## TL;DR

Chlomito is a new tool that accurately removes contamination from organelle genomes in nuclear genome assemblies, improving genome quality.

## Contribution

Chlomito introduces new metrics (ALCR and SDR) for precise identification and removal of organelle genome contamination.

## Key findings

- Chlomito accurately detects organelle-derived contigs in nuclear genome assemblies.
- The tool covers most regions of the organelle reference genomes, showing high efficiency and precision.
- Chlomito is packaged into a Docker image for user convenience and simplified workflow.

## Abstract

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.

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 transfer (HGT).

The accuracy of Chlomito was tested using sequencing data from Plum, Mango and Arabidopsis. The results confirmed that Chlomito can accurately detect contigs originating from the organelle genomes, and the identified contigs covered most regions of the organelle reference genomes, demonstrating efficiency and precision of Chlomito. Considering user convenience, we further packaged this method into a Docker image, simplified the data processing workflow.

Overall, Chlomito provides an efficient, accurate and convenient method for identifying and removing contigs derived from organelle genomes in genomic assembly data, contributing to the improvement of genome assembly quality.