Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
☆250Feb 5, 2026Updated 3 weeks ago
Alternatives and similar repositories for nextclade
Users that are interested in nextclade are comparing it to the libraries listed below
Sorting:
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation☆114Updated this week
- Software package for assigning SARS-CoV-2 genome sequences to global lineages.☆447Feb 19, 2026Updated last week
- Datasets for https://github.com/nextstrain/nextclade☆43Feb 16, 2026Updated last week
- Nextstrain build for mpox virus☆50Feb 16, 2026Updated last week
- SARS-Cov-2 Recombinant Finder for fasta sequences☆50Jun 22, 2022Updated 3 years ago
- A tool for exploring large trees in the browser☆123Feb 4, 2026Updated 3 weeks ago
- The ARTIC fieldbioinformatics pipeline☆129Jan 7, 2026Updated last month
- A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV…☆37Feb 4, 2026Updated 3 weeks ago
- snipit: summarise snps relative to your reference sequence☆167Jan 13, 2026Updated last month
- Reference-based consensus creation☆58Feb 10, 2026Updated 2 weeks ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆37Jan 22, 2026Updated last month
- Store of the trained model for pangolin to access.☆55Oct 4, 2022Updated 3 years ago
- Fast, scalable, accurate and accessible Bayesian phylogenetics☆42Updated this week
- Ultrafast Sample Placement on Existing Trees☆139Feb 6, 2026Updated 3 weeks ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36May 1, 2022Updated 3 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Feb 20, 2026Updated last week
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆52Jul 24, 2025Updated 7 months ago
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆28Feb 19, 2026Updated last week
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated 9 months ago
- a tool for designing primer panels for multiplex PCR.☆106Feb 5, 2024Updated 2 years ago
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆170Mar 22, 2023Updated 2 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆62Updated this week
- Nextstrain build for avian influenza viruses☆27Feb 13, 2026Updated 2 weeks ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆249Updated this week
- Depth-weighted De-Mixing☆127Updated this week
- ☆38Jan 12, 2026Updated last month
- baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development…☆116Feb 16, 2026Updated last week
- 🧬 Viral genome reference alignment☆12Jan 26, 2021Updated 5 years ago
- VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.☆20Sep 12, 2021Updated 4 years ago
- ☆17Jul 27, 2023Updated 2 years ago
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆134Feb 22, 2026Updated last week
- Pipeline components for real-time phylodynamic analysis☆275Updated this week
- Cluster Investigation & Virus Epidemiology Tool☆50Jun 17, 2025Updated 8 months ago
- ☆50Mar 11, 2022Updated 3 years ago
- This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…☆42Nov 20, 2019Updated 6 years ago
- Quality control for phylogenetic analyses☆13Updated this week
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Nov 8, 2023Updated 2 years ago
- Data and scripts for Zika virus tutorial☆10Oct 14, 2025Updated 4 months ago