Portable WDL workflows for CZ ID production pipelines
☆51Apr 23, 2026Updated 3 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☆19Jul 6, 2026Updated 3 weeks ago
- Tool to submit viral sequences to Genbank.☆16May 14, 2026Updated 2 months ago
- Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data☆60Feb 8, 2026Updated 5 months ago
- ☆27Aug 2, 2023Updated 2 years ago
- Portable WDL workflows for IDseq production pipelines☆32Jan 19, 2022Updated 4 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- ☆10Apr 16, 2025Updated last year
- viral-ngs: complete pipelines☆75Jul 9, 2026Updated 2 weeks ago
- VIGOR4☆22Aug 15, 2025Updated 11 months ago
- taxonomic classifier based on the kraken2 algorithms and more☆46Dec 12, 2025Updated 7 months ago
- ☆13Aug 20, 2025Updated 11 months ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆14Jun 30, 2023Updated 3 years ago
- Make coverage plots from bam files!☆15Mar 17, 2026Updated 4 months ago
- CZID (formerly IDseq) infectious disease command-line interface☆22Apr 8, 2026Updated 3 months ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated last year
- TAXnomic Profile Aggregation and STAndardisation☆44May 2, 2026Updated 2 months ago
- CFSAN Shigella Typing Pipeline☆15Jun 11, 2026Updated last month
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated last month
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆78Updated this week
- ☆28Updated this week
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆29Mar 10, 2026Updated 4 months ago
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆22Dec 9, 2025Updated 7 months ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆40Sep 22, 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.
- In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping☆66Jun 5, 2025Updated last year
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- ☆24Feb 2, 2026Updated 5 months ago
- Precise host read removal☆128Apr 13, 2026Updated 3 months 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
- Depth-weighted De-Mixing☆135Updated this week
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆27Jan 30, 2025Updated last year
- VirID: An integrated platform for the discovery and characterization of RNA Viruses☆26Jan 8, 2026Updated 6 months ago
- ☆23Jul 22, 2026Updated last week
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆15Aug 26, 2024Updated last year
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆16Feb 19, 2026Updated 5 months ago
- Host depletion optimised for clinical metagenomic sequencing applications☆19Jul 9, 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
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆16Jun 26, 2018Updated 8 years ago
- 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results☆252Jan 18, 2024Updated 2 years ago
- deduplicate FASTA and FASTQ files☆23Feb 16, 2022Updated 4 years ago