# OMD Curation Toolkit: a workflow for in-house curation of public omics datasets

## TL;DR

The OMD Curation Toolkit is a Python package that helps researchers curate public omics datasets by providing a standardized workflow for metadata and sequencing data.

## Contribution

The toolkit introduces a standardized, reusable workflow for in-house curation of public omics datasets.

## Key findings

- The OMD Curation Toolkit supports collection, control check, treatment, and integration of omics data.
- It is primarily focused on the European Nucleotide Archive but includes tools applicable to other data sources.
- The toolkit simplifies the curation process, enabling more efficient meta-analyses of sequencing data.

## Abstract

Major advances in sequencing technologies and the sharing of data and metadata in science have resulted in a wealth of publicly available datasets. However, working with and especially curating public omics datasets remains challenging despite these efforts. While a growing number of initiatives aim to re-use previous results, these present limitations that often lead to the need for further in-house curation and processing.

Here, we present the Omics Dataset Curation Toolkit (OMD Curation Toolkit), a python3 package designed to accompany and guide the researcher during the curation process of metadata and fastq files of public omics datasets. This workflow provides a standardized framework with multiple capabilities (collection, control check, treatment and integration) to facilitate the arduous task of curating public sequencing data projects. While centered on the European Nucleotide Archive (ENA), the majority of the provided tools are generic and can be used to curate datasets from different sources.

Thus, it offers valuable tools for the in-house curation previously needed to re-use public omics data. Due to its workflow structure and capabilities, it can be easily used and benefit investigators in developing novel omics meta-analyses based on sequencing data.

The online version contains supplementary material available at 10.1186/s12859-024-05803-9.