Nextclade
Nextclade: clade assignment, mutation calling and quality control for viral genomes - Published in JOSS (2021)
viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
https://github.com/bluebrain/bioexplorer
The Blue Brain BioExplorer (BBBE) is a tool for data visualization experts and scientists to extract and analyze scientific data from visualization and interactive exploration
black-hat-rust
Applied offensive security with Rust - https://kerkour.com/black-hat-rust
viralintegration
Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.
https://github.com/cbg-ethz/v-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
https://github.com/charlesfoster/ont-analysis-toolkit
A toolkit for monitoring ONT MinION sequencing, followed by data analysis, for viral genomes amplified with tiled amplicon sequencing.
https://github.com/cidgoh/nf-ncov-voc
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can be used to visualize the mutation profiles and functional annotations.
