DOI: 10.1093/bioinformatics/btae152 ISSN: 1367-4811
GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data
Eric Odle, Samual Kahng, Siratee Riewluang, Kyoko Kurihara, Kevin C Wakeman- Computational Mathematics
- Computational Theory and Mathematics
- Computer Science Applications
- Molecular Biology
- Biochemistry
- Statistics and Probability
Abstract
Motivation
Motivated by the challenges of decentralized genetic data spread across multiple international organizations, GINSA leverages the Global Biodiversity Information Facility (GBIF) infrastructure to automatically retrieve and link small ribosomal subunit (SSU) sequences with locality information.
Results
Testing on taxa from major organism groups demonstrates broad applicability across taxonomic levels and dataset sizes.
Availability
GINSA is a freely accessible Python program under the MIT License and can be installed from PyPI via pip.
Supplementary information
Supplementary data are available at Bioinformatics. Project code available at https://github.com/ericodle/GINSA.