Portable WDL workflows for CZ ID production pipelines
☆51Jun 17, 2025Updated 8 months ago
Alternatives and similar repositories for czid-workflows
Users that are interested in czid-workflows are comparing it to the libraries listed below
Sorting:
- Repo for PrimerSchemes☆17Feb 24, 2026Updated 2 weeks ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Rapidly extract reads from a FASTQ file based on taxonomic classification via Kraken2.☆13Jan 26, 2026Updated last month
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆13Jun 30, 2023Updated 2 years ago
- ☆10Apr 16, 2025Updated 10 months ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last week
- ☆11Mar 10, 2024Updated 2 years ago
- ☆27Aug 2, 2023Updated 2 years ago
- VIGOR4☆21Aug 15, 2025Updated 6 months ago
- viral-ngs: complete pipelines☆73Feb 27, 2026Updated last week
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated 2 weeks ago
- Make coverage plots from bam files!☆14Feb 20, 2026Updated 2 weeks ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆62Updated this week
- taxonomic classifier based on the kraken2 algorithms and more☆46Dec 12, 2025Updated 2 months ago
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆21Dec 9, 2025Updated 3 months ago
- ☆21Updated this week
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆13Aug 26, 2024Updated last year
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Sep 22, 2022Updated 3 years ago
- Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data☆59Feb 8, 2026Updated last month
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated last month
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆26Jan 30, 2025Updated last year
- TAXnomic Profile Aggregation and STAndardisation☆42Nov 18, 2025Updated 3 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping☆65Jun 5, 2025Updated 9 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆42Sep 3, 2024Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 7 months ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆32Apr 24, 2025Updated 10 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 2 years ago
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆28Feb 19, 2026Updated 2 weeks ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆27Aug 26, 2024Updated last year
- Bifrost graph gene caller.☆98Jan 20, 2026Updated last month
- 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results☆244Jan 18, 2024Updated 2 years ago
- Precise host read removal☆117Sep 4, 2025Updated 6 months ago
- A functional profiler for metagenomes using FracMinHash☆21Jul 14, 2025Updated 7 months ago
- ☆26Updated this week
- Chimera: A Versatile Metagenomic Classification Tool☆21Feb 1, 2026Updated last month