SUMMARY: Snipit is an analysis and visualization tool designed for summarizing single nucleotide polymorphisms in sequences in comparison to a reference sequence. This tool efficiently catalogues nucleotide and amino acid differences, enabling clear comparisons through customizable, publication-ready figures. With features such as configurable colour palettes, customizable record sorting, and the ability to output figures in multiple formats, snipit offers a user-friendly interface for researchers across diverse disciplines. In addition, snipit includes a specialized recombi-mode for illustrating recombination patterns, which can highlight otherwise often difficult-to-detect relationships between sequences. AVAILABILITY AND IMPLEMENTATION: Snipit is an open-source python-based tool that is hosted on GitHub under a GNU-GPL 3.0 licence (https://github.com/aineniamh/snipit). It can be installed from PyPi using pip. Source code and additional documentation can be found on the GitHub repository.

SUMMARY: Scorpio provides a set of command line utilities for classifying, haplotyping, and defining constellations of mutations for an aligned set of genome sequences. It was developed to enable exploration and classification of variants of concern within the SARS-CoV-2 pandemic, but can be applied more generally to other species. AVAILABILITY AND IMPLEMENTATION: Scorpio is an open-source project distributed under the GNU GPL version 3 license. Source code and binaries are available at https://github.com/cov-lineages/scorpio, and binaries are also available from Bioconda. SARS-CoV-2 specific definitions can be installed as a separate dependency from https://github.com/cov-lineages/constellations.

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:[email protected].