OMD Curation Toolkit: a workflow for in-house curation of public omics datasets.
BMC Bioinformatics
; 25(1): 184, 2024 May 09.
Article
in En
| MEDLINE
| ID: mdl-38724907
ABSTRACT
BACKGROUND:
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.RESULTS:
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.CONCLUSIONS:
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.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Workflow
/
Data Curation
Language:
En
Journal:
BMC Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2024
Document type:
Article
Affiliation country:
España
Country of publication:
Reino Unido