The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.
☆28Mar 20, 2026Updated this week
Alternatives and similar repositories for cli
Users that are interested in cli are comparing it to the libraries listed below
Sorting:
- Umbrella documentation project for Nextstrain☆18Updated this week
- Pipeline components for real-time phylodynamic analysis☆276Updated this week
- Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments☆10Mar 13, 2021Updated 5 years ago
- Nextstrain build for Zika virus☆10Dec 19, 2025Updated 3 months ago
- interactive phylogenetic tree viewer☆11Jun 26, 2024Updated last year
- serious constellations of reoccurring phylogenetically-independent origin☆39Feb 13, 2026Updated last month
- MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation☆23Mar 13, 2026Updated last week
- An API, a query engine, and a database schema for genomic sequences; currently with a focus on SARS-CoV-2☆31Updated this week
- Determining tandem repeat lengths using raw nanopore signals.☆15Sep 11, 2023Updated 2 years ago
- computational training at Fred Hutch☆12Jun 11, 2021Updated 4 years ago
- Nextstrain build for mpox virus☆50Updated this week
- Scripts. config, and snakefiles for seasonal-flu nextstrain builds☆59Updated this week
- Data and scripts for Zika virus tutorial☆10Oct 14, 2025Updated 5 months ago
- ☆13Nov 26, 2025Updated 3 months ago
- CouchDB library for node and the browser☆16Jun 15, 2015Updated 10 years ago
- ☆20Mar 28, 2017Updated 8 years ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated 10 months ago
- LocusCompare is an interactive visualization tool for comparing two genetic association datasets.☆21Apr 8, 2023Updated 2 years ago
- Data and workflow examples☆16Apr 9, 2018Updated 7 years ago
- Nextstrain build for SARS-CoV-2☆1,360Mar 2, 2026Updated 2 weeks ago
- A cloud-based deployment of the 10x Genomics Cell Ranger software☆14Jul 7, 2019Updated 6 years ago
- Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R☆32Feb 23, 2026Updated 3 weeks ago
- Intuitive OOP wrapper for command-line processes; uses PTY to avoid buffering.☆14Mar 8, 2026Updated last week
- Contains sample scripts and code to be used with LabKey Server☆11Feb 19, 2026Updated last month
- Software for preprocessing, filtering, alignment, and reporting of smallRNA-seq datasets☆23Apr 5, 2023Updated 2 years ago
- Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates☆21Nov 8, 2024Updated last year
- Documentation of the Snakemake-Profiles project.☆55Mar 15, 2022Updated 4 years ago
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆170Mar 22, 2023Updated 2 years ago
- Racmacs R package for performing antigenic cartography☆24Jun 27, 2024Updated last year
- A munin node written in pure python☆10Mar 14, 2013Updated 13 years ago
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆252Mar 10, 2026Updated last week
- twango = Django ORM + Twisted - Blocking☆20Oct 4, 2017Updated 8 years ago
- CiteFuse:☆28Feb 7, 2023Updated 3 years ago
- A project to convert the default and contrib.humanize template filters from Django to JavaScript☆14Mar 9, 2026Updated last week
- A Library for Denoising Single-Cell Data with Random Matrix Theory☆38Aug 16, 2023Updated 2 years ago
- Common methods to help create fabric deplopment scripts for django☆35Jan 28, 2010Updated 16 years ago
- Zunda: Japanese Enhanced Modality Analyzer client for Python.☆10Nov 30, 2019Updated 6 years ago
- Sets up GitLab 5.3 on Ubuntu 12.10☆50Aug 29, 2013Updated 12 years ago
- Images for Saturn Cloud☆12Dec 18, 2025Updated 3 months ago