SynthesisBioinformatics (Oxford, England)2022
Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue.
Synthesis in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- A conserved bacterial signature characterizes plant microbiome responses to drought.Frontiers in microbiology · 2026Article
- ViromeXplore: integrative workflows for complete and reproducible virome characterization.Briefings in bioinformatics · 2025Article
- Common microbial signatures in blood and their amplification in clinical disorders.Gut microbes reports · 2025Review
- Differential impact ofHeliyon · 2024Article
- Article
- Article
- Impact of methane mitigation strategies on the native ruminant microbiome: A protocol for a systematic review and meta-analysis.PloS one · 2024Article
- Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay.PLoS computational biology · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationThe volume of public nucleotide sequence data has blossomed over the past two decades and is ripe for re- and meta-analyses to enable novel discoveries. However, reproducible re-use and management of sequence datasets and associated metadata remain critical challenges. We created the open source Python package q2-fondue to enable user-friendly acquisition, re-use and management of public sequence (meta)data while adhering to open data principles.
resultsq2-fondue allows fully provenance-tracked programmatic access to and management of data from the NCBI Sequence Read Archive (SRA). Unlike other packages allowing download of sequence data from the SRA, q2-fondue enables full data provenance tracking from data download to final visualization, integrates with the QIIME 2 ecosystem, prevents data loss upon space exhaustion and allows download of (meta)data given a publication library. To highlight its manifold capabilities, we present executable demonstrations using publicly available amplicon, whole genome and metagenome datasets. AVAILABILITY AND IMPLEMENTATION: q2-fondue is available as an open-source BSD-3-licensed Python package at https://github.com/bokulich-lab/q2-fondue. Usage tutorials are available in the same repository. All Jupyter notebooks used in this article are available under https://github.com/bokulich-lab/q2-fondue-examples. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.