Collection of R scripts for SARS-CoV-2 (variant) analyses
☆12Mar 2, 2023Updated 3 years ago
Alternatives and similar repositories for SARS-CoV-2-analyses
Users that are interested in SARS-CoV-2-analyses are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- SARS-CoV-2 workflow for nanopore sequence data☆42Jul 17, 2026Updated last week
- Course materials for an introduction to SARS-CoV-2 sequencing data analysis☆14Aug 15, 2024Updated last year
- Luslab nextflow modules☆14Apr 30, 2021Updated 5 years ago
- Harmonization of AMR predictor tool outputs☆25Jan 14, 2025Updated last year
- DegenPrimer is a tool to check the quality of degenerate primers by simulating PCR☆17May 12, 2022Updated 4 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Full-length de novo viral haplotype reconstruction from noisy long reads☆21Nov 6, 2023Updated 2 years ago
- Tool for analysing viral diversity from High Throughput Sequencing☆12Nov 20, 2025Updated 8 months ago
- Influenza genome analysis Nextflow workflow☆33Sep 15, 2025Updated 10 months ago
- breakfast is a simple and fast tool for clustering SARS-CoV-2 genomes using precalculated sequence features (e.g. nucleotide substitution…☆11Jul 1, 2026Updated 3 weeks ago
- Primalscheme3. Generation of highly multiplex primerschemes☆26Dec 4, 2025Updated 7 months ago
- A Nextflow full-length 16S profiling pipeline for ONT reads☆25Nov 16, 2023Updated 2 years ago
- Hybridization probe design for targeted genomic sequencing of diverse and hypervariable viral taxa☆25May 30, 2023Updated 3 years ago
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 6 years ago
- ☆11Jun 29, 2023Updated 3 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆54Mar 23, 2026Updated 4 months ago
- The ARTIC fieldbioinformatics pipeline☆134Jul 16, 2026Updated last week
- Simple Manipulation Of Trees☆14Aug 16, 2025Updated 11 months ago
- ☆15May 21, 2026Updated 2 months ago
- finding conserved regions in highly diverse genomes☆16May 25, 2026Updated 2 months ago
- An RNA virus strain-level identification tool for short reads.☆23Apr 6, 2026Updated 3 months ago
- ☆38Jan 12, 2026Updated 6 months ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated last month
- Repo for PrimerSchemes☆19Jul 6, 2026Updated 3 weeks ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 8 months ago
- MetaPORE – Chiu Laboratory, University of California, San Francisco☆12Nov 4, 2015Updated 10 years ago
- Real-time species-typing visualisation for nanopore data.☆12Apr 11, 2023Updated 3 years ago
- Workflow for viral analysis guided by reference☆17Jun 9, 2026Updated last month
- Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.☆15Jul 6, 2026Updated 3 weeks ago
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆58Apr 1, 2025Updated last year
- VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.☆20Sep 12, 2021Updated 4 years ago
- Tool to submit viral sequences to Genbank.☆16May 14, 2026Updated 2 months ago
- 🧬 Viral genome reference alignment☆12Jan 26, 2021Updated 5 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Package to design primers for MutaSeq and related methods☆11Jan 15, 2021Updated 5 years ago
- de.NBI Nanopore Training Course☆21Jun 13, 2025Updated last year
- ☆12Dec 22, 2025Updated 7 months ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆40Apr 6, 2026Updated 3 months ago
- Automated Rice Variant calling workflow for HPC, Cloud and Desktop systems.☆13May 11, 2024Updated 2 years ago
- De novo assembly of nanopore reads using nextflow☆20Aug 5, 2020Updated 5 years ago
- ☆36Nov 11, 2022Updated 3 years ago