Metadata retrieval from sequence databases with ffq
Ángel Gálvez-MerchániD, Kyung Hoi MiniD, Lior S. PachteriD, A. Sina BooeshaghiiD
Abstract
We present a command-line tool, called ffq, for querying user-generated data and metadata from sequence databases. The code can be found here: https://github.com/pachterlab/ffq.
02 /Specification & Classification
Click any tag to browse matching papers- Citations
- 35
- FWCI
- 2.45
- Field percentile
- top 9%
- Research Focus
- Approach
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- iSeq: An integrated tool to fetch public sequencing data
Haoyu Chao, Z Li, … Ming Chen·BioinformaticsPeer-reviewed·Oct 23, 2024
- Reproducible acquisition, management, and meta-analysis of nucleotide sequence (meta)data using q2-fondue
Michał Ziemski, Anja Adamov, … Nicholas A. Bokulich·BioinformaticsPeer-reviewed·Sep 19, 2022
- SeqDesk: a sequencing-facility management system for standards-compliant and FAIR (meta)data submission
Philipp C. Münch, Gary Robertson, Alice Carolyn McHardy·bioRxiv·Aug 11, 2026
- MMseqs2 desktop and local web server app for fast, interactive sequence searches
Milot Mirdita, Martin Steinegger, Johannes Söding·BioinformaticsPeer-reviewed·Jan 4, 2019
- The Backpack Quotient Filter: a dynamic and space-efficient data structure for querying k-mers with abundance.
Victor Levallois, Francesco Andreace, … Pierre Peterlongo·iSciencePeer-reviewed·Nov 22, 2024
- PubData: search engine for bioinformatics databases worldwide
Bohdan B. Khomtchouk, Kasra A. Vand, … Claes Wahlestedt·bioRxiv·Aug 16, 2016