CZID (formerly IDseq) infectious disease command-line interface
☆21Apr 8, 2026Updated last month
Alternatives and similar repositories for czid-cli
Users that are interested in czid-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:
- Portable WDL workflows for IDseq production pipelines☆32Jan 19, 2022Updated 4 years ago
- Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data☆60Feb 8, 2026Updated 3 months ago
- MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data☆13Jan 28, 2026Updated 3 months ago
- Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.☆13Jun 3, 2025Updated 11 months ago
- Highly sensitive pathogen detection☆12Oct 5, 2020Updated 5 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Microbial agile accurate SNP Typer☆30Dec 27, 2023Updated 2 years ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated 2 years ago
- Opinionated viral metagenomics workflow☆14Updated this week
- Portable WDL workflows for CZ ID production pipelines☆51Apr 23, 2026Updated last month
- Infectious Disease Sequencing Platform☆90Feb 10, 2026Updated 3 months ago
- ☆24Updated this week
- Reference-based consensus creation☆61Updated this week
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆26Sep 12, 2024Updated last year
- ☆13Aug 15, 2025Updated 9 months ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- deduplicate FASTA and FASTQ files☆23Feb 16, 2022Updated 4 years ago
- A tooL for Prokaryotic Phylogeny And Clustering Analysis☆13Updated this week
- Mycobacterium tuberculosis complex lineage typing☆10Jun 22, 2025Updated 11 months ago
- ☆11Dec 19, 2024Updated last year
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆14Jun 12, 2024Updated last year
- GPU-accelerated DNA barcode classification☆14Jan 2, 2025Updated last year
- a tool for designing primer panels for multiplex PCR.☆108Feb 5, 2024Updated 2 years ago
- ☆11Nov 17, 2020Updated 5 years ago
- Whole genome focused array SNP typer☆14Feb 2, 2026Updated 3 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- ☆16Feb 5, 2025Updated last year
- Bact-Builder: Microbial de novo genome assembly pipeline☆13Dec 5, 2022Updated 3 years ago
- Example code for calling Panther API services☆13Dec 12, 2023Updated 2 years ago
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.☆14May 12, 2024Updated 2 years ago
- hecatomb is a virome analysis pipeline for analysis of Illumina sequence data☆60Sep 23, 2025Updated 8 months ago
- This is a simple introductory tutorial to help you get started with using BEAST2 and its accomplices.☆11Jul 8, 2025Updated 10 months ago
- UPHL's Reference Free Pipeline☆28Updated this week
- Snakemake pipeline for simulating shotgun metagenomic samples☆29Mar 13, 2026Updated 2 months ago
- MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read M…☆13Jul 2, 2022Updated 3 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Assembly and intrahost/low-frequency variant calling for viral samples☆163May 13, 2026Updated last week
- ☆12May 6, 2021Updated 5 years ago
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆29Mar 10, 2026Updated 2 months ago
- Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins☆15Dec 7, 2021Updated 4 years ago
- ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then sear…☆31Jan 24, 2025Updated last year
- Primer design from single genes to whole gene families for unlocking the tree of life☆16May 14, 2026Updated last week
- Assessing the quality of genomes using busco☆14Mar 23, 2023Updated 3 years ago