# esloco: simulation-based estimation of local coverage in long-read DNA sequencing

## TL;DR

esloco is a simulation tool that helps predict DNA sequencing coverage in long-read experiments, reducing the need for costly pilot studies.

## Contribution

esloco introduces a Monte Carlo-based framework for estimating local coverage in long-read sequencing, even for unknown target regions.

## Key findings

- esloco accurately predicts local coverage based on sequencing depth and read length distribution.
- Benchmarking on a 45-gene panel showed strong agreement with real sequencing data.
- The tool supports PCR-free and unknown target region scenarios like viral integration and CRISPR-Cas9.

## Abstract

Long-read DNA sequencing is increasingly applied for whole-genome studies, yet experimental planning often lacks reliable estimates of target region coverage, leading to costly and time-consuming pilot studies and replicates. We present esloco, a Monte Carlo-based simulation framework for estimating local coverage in long-read sequencing experiments, including scenarios with unknown target regions (e.g. viral integration, CRISPR-Cas9) or PCR-free designs (e.g. base modifications). By modeling coverage as a function of sequencing depth and read length distribution, esloco enables informed predictions of local sequencing outcomes. Benchmarking across a 45-gene panel demonstrated close agreement with empirical data, underscoring the framework’s reliability.

esloco is a Python package available on PyPI (https://pypi.org/project/esloco/), GitHub (https://github.com/aweich/esloco), and Zenodo (https://doi.org/10.5281/zenodo.17776161).