SPEAR

'SPEAR' is a software tool designed for rapid and lightweight annotation and scoring of SARS-CoV-2 variants. It focuses on identifying mutations that may contribute to potential immune escape and transmissibility at the time of sequencing. This tool is particularly useful for genomic surveillance and allows users to evaluate results in real-time. It provides interactive data visualization for comprehensive reporting.

Key features of SPEAR:
1. SARS-CoV-2 Variant Analysis: SPEAR is tailored for the analysis of SARS-CoV-2 variants, particularly mutations that may affect the virus's interactions with the immune system (potential immune escape) and its ability to bind to the ACE2 receptor (transmissibility).
2. Real-Time Genomic Surveillance: Researchers and public health officials can use SPEAR to analyze genomic surveillance data as it becomes available, allowing for timely and informed decision-making.
3. Interactive Data Visualization: The tool offers powerful data visualization capabilities, making it easier to interpret and explore the results.

Topic

Genetic variation;Genomics;Transcription factors and regulatory sites;Mapping

Detail

  • Operation: Phylogenetic tree annotation;Variant calling;Sequencing quality control;Sequence trimming

  • Software interface: Command-line user interface

  • Language: Python

  • License: The MIT Licence

  • Cost: Free

  • Version name: v1.1.3

  • Credit: COG-UK, the Research England’s Expanding Excellence in England (E3) Fund, the UK Health Security Agency.

  • Input: -

  • Output: -

  • Contact: Matthew Bashton matthew.bashton@northumbria.ac.uk

  • Collection: -

  • Maturity: -

Publications

Download and documentation

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