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.
☆28May 20, 2026Updated this week
Alternatives and similar repositories for cli
Users that are interested in cli are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Nextstrain build for avian influenza viruses☆28Apr 20, 2026Updated last month
- Umbrella documentation project for Nextstrain☆18Updated this week
- Nextflow workflow template repository☆20Mar 12, 2026Updated 2 months ago
- 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
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Nextstrain build for Zika virus☆10Apr 20, 2026Updated last month
- An API, a query engine, and a database schema for genomic sequences; currently with a focus on SARS-CoV-2☆31May 14, 2026Updated last week
- MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation☆23Apr 1, 2026Updated last month
- 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☆62May 11, 2026Updated last week
- Data and scripts for Zika virus tutorial☆10Oct 14, 2025Updated 7 months ago
- ☆13Updated this week
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)☆27Jul 19, 2022Updated 3 years ago
- ☆20Mar 28, 2017Updated 9 years ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated last year
- LocusCompare is an interactive visualization tool for comparing two genetic association datasets.☆22Apr 8, 2023Updated 3 years ago
- Data and workflow examples☆16Apr 9, 2018Updated 8 years ago
- Nextstrain build for SARS-CoV-2☆1,359May 7, 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 2 months ago
- Intuitive OOP wrapper for command-line processes; uses PTY to avoid buffering.☆14Mar 8, 2026Updated 2 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Official place for proposals and details around monkeypox virus lineage designations☆23Dec 9, 2025Updated 5 months ago
- Contains sample scripts and code to be used with LabKey Server☆11Feb 19, 2026Updated 3 months ago
- A tool for exploring large trees in the browser☆132May 7, 2026Updated 2 weeks 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☆171Mar 22, 2023Updated 3 years ago
- Racmacs R package for performing antigenic cartography☆24Jun 27, 2024Updated last year
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆254May 5, 2026Updated 2 weeks ago
- A Library for Denoising Single-Cell Data with Random Matrix Theory☆39Aug 16, 2023Updated 2 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Sets up GitLab 5.3 on Ubuntu 12.10☆50Aug 29, 2013Updated 12 years ago
- Butler is a framework for running scientific workflows on public and academic clouds.☆70Feb 10, 2020Updated 6 years ago
- AWS Biotech Blueprint Multi-Account☆12Jul 22, 2020Updated 5 years ago
- Images for Saturn Cloud☆12Dec 18, 2025Updated 5 months ago
- Utility CSS and JavaScript for R Markdown☆13Jan 18, 2021Updated 5 years ago
- ☆14May 30, 2023Updated 2 years ago
- forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research☆37Apr 1, 2026Updated last month