Lees WD, Saha S, Yaari G, Watson CT. Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies.
Bioinformatics 2024;
40:btae144. [PMID:
38478393 PMCID:
PMC10957512 DOI:
10.1093/bioinformatics/btae144]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/11/2024] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Abstract
SUMMARY
Knowledge of immunoglobulin and T cell receptor encoding genes is derived from high-quality genomic sequencing. High-throughput sequencing is delivering large volumes of data, and precise, high-throughput approaches to annotation are needed. Digger is an automated tool that identifies coding and regulatory regions of these genes, with results comparable to those obtained by current expert curational methods.
AVAILABILITY AND IMPLEMENTATION
Digger is published under open source license at https://github.com/williamdlees/Digger and is available as a Python package and a Docker container.
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