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Published, Version of Record (VoR)CC BY V4.0, Open
Journal article
ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data
Frontiers in immunology, v 9, pp 2107-2107
21 Sep 2018
PMID: 30298069
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
ImmuneDB is a system for storing and analyzing high-throughput immune receptor sequencing data. Unlike most existing tools, which utilize flat-files, ImmuneDB stores data in a well-structured MySQL database, enabling efficient data queries. It can take raw sequencing data as input and annotate receptor gene usage, infer clonotypes, aggregate results, and run common downstream analyses such as calculating selection pressure and constructing clonal lineages. Alternatively, pre-annotated data can be imported and analyzed data can be exported in a variety of common Adaptive Immune Receptor Repertoire (AIRR) file formats. To validate ImmuneDB, we compare its results to those of another pipeline, MiXCR. We show that the biological conclusions drawn would be similar with either tool, while ImmuneDB provides the additional benefits of integrating other common tools and storing data in a database. ImmuneDB is freely available on GitHub at
https://github.com/arosenfeld/immunedb
, on PyPi at
https://pypi.org/project/ImmuneDB
, and a Docker container is provided at
https://hub.docker.com/r/arosenfeld/immunedb
. Full documentation is available at
http://immunedb.com
.
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Details
- Title
- ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data
- Creators
- Aaron M. Rosenfeld - Drexel UniversityWenzhao Meng - University of PennsylvaniaEline T. Luning Prak - , , , , , , , ,Uri Hershberg - University of Haifa
- Publication Details
- Frontiers in immunology, v 9, pp 2107-2107
- Publisher
- Frontiers Media S.A
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000445237200001
- Scopus ID
- 2-s2.0-85054779808
- Other Identifier
- 991019167661604721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Immunology