Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
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Jan 16, 2025 - Python
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virology
Here are 21 public repositories matching this topic...
Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.
surveillance ngs clinical metagenomics public-health diagnostics viruses erasmus virology rivm viromics virus-typing
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Sep 1, 2023 - Python
genetic distance plotting for recombination events analysis
python bioinformatics alignment genetic-distances virology dna-recombination recombination-events distance-plots
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Nov 21, 2024 - Python
FluMut is a command-line tool to find markers of interest in H5N1 avian influenza viruses.
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May 21, 2025 - Python
SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.
python bioinformatics snakemake public-health viruses virology ngs-analysis snakemake-workflow rivm consensus-sequences coronavirus coronavirus-analysis
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Jul 3, 2024 - Python
ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome
python bioinformatics snakemake analysis public-health viruses virology ngs-analysis snakemake-workflow rivm consensus-sequences
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Jun 6, 2025 - Python
The art of decorating a phage genome by gluing feature cutouts into it.
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Oct 4, 2022 - Python
TrueConsense is a consensus caller for viral-targets that create biologically correct consensus sequences. TrueConsense keeps track of open reading frames, compensates for common sequencing or alignment artefacts, and is able to generate consensus sequences on multiple coverage-thresholds at the same time
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Jan 27, 2025 - Python
NGS data analysis scripts for HBV elimination research group
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Jun 23, 2021 - Python
Git-based viral taxonomy management system - track changes, migrate datasets, and cite specific versions. Website: https://shandley.github.io/ICTV-git/
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Jun 11, 2025 - Python
NGS data analysis scripts for HBV elimination research group
visualization bioinformatics python3 fasta sequence-alignment virology hbv ngs-analysis hbv-mutations
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Jun 22, 2022 - Python
Fitness estimates of SARS-CoV-2 variants
epidemiology forecasting-models fitness-landscape virology statistical-modeling sars-cov-2 wastewater-surveillance wastewater-based-epidemiology
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Jun 4, 2025 - Python
Master cutting-edge genomics and bioinformatics approaches to advance viral diagnostics and investigation
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Mar 10, 2025 - Python
glimmer - genetics information gathering CLI tool.
bioinformatics microbiology command-line-tool research-and-development bioinformatics-analysis virology research-companion
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Jul 23, 2021 - Python
An influenza virus model examining the effects of cellular regeneration on cell-to-cell and cell-free viral transmission.
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Dec 29, 2022 - Python
A Panel progressive web app for synonymous recoding of viral genomes with CpG dinucleotides
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Apr 3, 2024 - Python
🔬 2.3.4.4b H5N1 Mammalian Adaptation Analysis Computational pipeline for analyzing host-specific mutations and selection pressures in 2.3.4.4b H5N1 influenza A virus (IAV). Includes sequence processing, evolutionary modeling (MEME analysis), and visualization tools (heatmaps, radar plots) to assess the pandemic potential of avian-origin strains
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Jun 1, 2025 - Python
Bioinformatics tool for inFLUenza REassortments Detection, including zoonotic segments.
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Sep 19, 2024 - Python
A web tool for recombination events analysis in viral genomes. Django based version of recan
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Dec 8, 2024 - Python
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