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. 2024 Mar 29;40(4):btae152.
doi: 10.1093/bioinformatics/btae152.

GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data

Eric Odle  1 , Samuel Kahng  2   3 , Siratee Riewluang  1 , Kyoko Kurihara  1 , Kevin C Wakeman  3   4
Affiliations

GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data

Eric Odle et al. Bioinformatics. .

Abstract

Motivation: Motivated by the challenges of decentralized genetic data spread across multiple international organizations, GINSA leverages the Global Biodiversity Information Facility infrastructure to automatically retrieve and link small ribosomal subunit sequences with locality information.

Results: Testing on taxa from major organism groups demonstrates broad applicability across taxonomic levels and dataset sizes.

Availability and implementation: GINSA is a freely accessible Python program under the MIT License and can be installed from PyPI via pip.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
Chart visualizing the GINSA workflow. User input is taken as a GBIF search taxon. Occurrences are then linked with their source sequences archived on ENA. Output CSV and FASTA files link GBIF occurrence IDs, localities, and sequences.
See this image and copyright information in PMC

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