Portable WDL workflows for CZ ID production pipelines
☆53Apr 23, 2026Updated 6 months ago
Alternatives and similar repositories for czid-workflows
Users that are interested in czid-workflows are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Repo for PrimerSchemes☆22Oct 27, 2026Updated 2 weeks ago
- VIGOR4☆24Aug 15, 2025Updated last year
- This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…☆44Nov 20, 2019Updated 6 years ago
- Portable WDL workflows for IDseq production pipelines☆32Jan 19, 2022Updated 4 years ago
- A GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences.☆29Jun 4, 2024Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Tool to submit viral sequences to Genbank.☆16May 14, 2026Updated 6 months ago
- Host depletion optimised for clinical metagenomic sequencing applications☆19Jul 9, 2026Updated 4 months ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆40Sep 22, 2022Updated 4 years ago
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆29Oct 20, 2026Updated 3 weeks ago
- TAXnomic Profile Aggregation and STAndardisation☆43May 2, 2026Updated 6 months ago
- Precise host read removal☆134Apr 13, 2026Updated 7 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and give confidences of microbial organisms within short- or long-read…☆85Updated this week
- ☆37Oct 30, 2026Updated 2 weeks ago
- Basestack is a platform for rapid and real time analysis of NGS data. It provides a executable application that connects standard bionfor…☆27Jan 7, 2025Updated last year
- 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.
- A Python package for working with Bactopia☆12Aug 5, 2026Updated 3 months ago
- Easy installation for INSaFLU made by docker☆10Oct 1, 2026Updated last month
- ☆13Aug 20, 2025Updated last year
- Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data☆60Updated this week
- ☆28Aug 2, 2023Updated 3 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆42Nov 3, 2026Updated last week
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated 2 years ago
- taxonomic classifier based on the kraken2 algorithms and more☆46Dec 12, 2025Updated 11 months ago
- 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results☆249Jan 18, 2024Updated 2 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆27Jan 30, 2025Updated last year
- ☆10Apr 16, 2025Updated last year
- Depth-weighted De-Mixing☆134Updated this week
- Infectious Disease Sequencing Platform☆91Feb 10, 2026Updated 9 months ago
- CFSAN Shigella Typing Pipeline☆15Jun 11, 2026Updated 5 months ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Oct 27, 2026Updated 2 weeks ago
- Make coverage plots from bam files!☆16Mar 17, 2026Updated 7 months ago
- Trim lots of metagenomics samples all at once☆10May 2, 2024Updated 2 years ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 3 years ago
- 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.
- Assembly and intrahost/low-frequency variant calling for viral samples☆167Updated this week
- Opinionated viral metagenomics workflow☆20Oct 8, 2026Updated last month
- Nextflow version of SNVPhyl☆12Oct 24, 2024Updated 2 years ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆14Jun 30, 2023Updated 3 years ago
- viral-ngs: complete pipelines☆75Oct 24, 2026Updated 3 weeks ago
- Nextflow pipeline for bacterial clustering and linkage detection based on core genome analysis, designed to support genomic surveillance …☆12Updated this week
- mgikit is a collection of tools used to demultiplex fastq files and generate demultiplexing and quality reports.☆20Nov 4, 2026Updated last week
Are these results useful?