Reference-based consensus creation
☆61Aug 11, 2026Updated this week
Alternatives and similar repositories for Cecret
Users that are interested in Cecret are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- UPHL's Reference Free Pipeline☆29Updated this week
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated 2 months ago
- Assembly of Nanopore Sequencing☆17May 21, 2026Updated 2 months ago
- 🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens☆110Updated this week
- Extract subsets of ONT (Nanopore) reads based on time☆25Sep 12, 2024Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆24Feb 2, 2026Updated 6 months ago
- Python Toolkit for using containerized programs in either Singularity or Docker☆31Mar 19, 2024Updated 2 years ago
- emm Automatic Isolate Labeller☆15Mar 25, 2025Updated last year
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆15Jun 5, 2026Updated 2 months ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated 2 years ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- ☆27Aug 2, 2023Updated 3 years ago
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆29Mar 10, 2026Updated 5 months ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆41Apr 6, 2026Updated 4 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆23Jul 22, 2026Updated 3 weeks ago
- ☆30Mar 6, 2025Updated last year
- Bacterial surveillance pipeline.☆28Updated this week
- MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates☆94Jul 23, 2026Updated 3 weeks ago
- ☆10Apr 16, 2025Updated last year
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation☆119Jun 18, 2026Updated last month
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.☆16Updated this week
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆65Updated this week
- TaxTriage is a Nextflow workflow designed to agnostically identify and give confidences of microbial organisms within short- or long-read…☆80Updated this week
- 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.
- Rapid determination of appropriate reference genomes.☆102Jan 22, 2025Updated last year
- Dockerfiles and documentation on tools for public health bioinformatics☆225Updated this week
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆15Jun 14, 2022Updated 4 years ago
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆20Updated this week
- A simple pipeline for bacterial assembly and quality control☆16Updated this week
- Assembly and intrahost/low-frequency variant calling for viral samples☆167Aug 6, 2026Updated last week
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆14Jan 6, 2023Updated 3 years ago
- ☆15Jun 30, 2021Updated 5 years ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Standard database for the TBProfiler tool☆30Jun 23, 2026Updated last month
- Viral (meta)-genome assembly pipeline.☆23Jul 22, 2026Updated 3 weeks ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆55Jul 24, 2025Updated last year
- IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.☆28Jul 6, 2026Updated last month
- Influenza genome analysis Nextflow workflow☆27Jun 3, 2026Updated 2 months ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆40Updated this week
- Variant calling pipeline designed for Q20+ ONT long-reads☆15Jan 23, 2026Updated 6 months ago