SC2 variant detection and composition pipeline
☆19Jul 14, 2023Updated 2 years ago
Alternatives and similar repositories for C-WAP
Users that are interested in C-WAP are comparing it to the libraries listed below
Sorting:
- Depth-weighted De-Mixing☆128Updated this week
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- Repository containing a method for automatically identifying pathogen lineages from a phylogeny.☆17May 19, 2023Updated 2 years ago
- ☆27Aug 2, 2023Updated 2 years ago
- MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation☆23Sep 30, 2025Updated 5 months ago
- ☆12Jul 21, 2025Updated 7 months ago
- 🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens☆96Updated this week
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆14Jun 14, 2022Updated 3 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 7 months ago
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.☆16Updated this week
- ASMNGS20 - 2020 Conference Details☆15Jun 10, 2022Updated 3 years ago
- A simple pipeline for bacterial assembly and quality control☆16Feb 26, 2026Updated last week
- A SARS-CoV-2 Mutation Pattern Query Tool☆17Mar 21, 2023Updated 2 years ago
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆134Feb 27, 2026Updated last week
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆60Mar 23, 2023Updated 2 years ago
- Methods to determine sequence element (unitig) presence/absence☆23Nov 24, 2025Updated 3 months ago
- Assign genotypes to Salmonella Paratyphi A isolates using their whole-genome data.☆10Mar 6, 2025Updated last year
- In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data☆22May 8, 2024Updated last year
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- Interpretative standards for AMR genotypes☆27Updated this week
- ☆22Feb 2, 2026Updated last month
- Data repository for NWSS☆19Feb 18, 2026Updated 2 weeks ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆10Sep 27, 2025Updated 5 months ago
- Metagenomics Pipeline Repository for January, 2015 NCBI/ADDS Hackathon at NIH☆10Oct 31, 2016Updated 9 years ago
- ☆10Apr 16, 2025Updated 10 months ago
- ARTIC SARS-CoV-2 workflow and reporting☆50Apr 25, 2025Updated 10 months ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆61Feb 27, 2026Updated last week
- Some simple scripts to ease management and local basecalling of millions of FAST5 files☆25Nov 25, 2017Updated 8 years ago
- UPHL's Reference Free Pipeline☆27Updated this week
- Tool for analysing viral diversity from High Throughput Sequencing☆12Nov 20, 2025Updated 3 months ago
- Docker image build for nextstrain/base☆12Updated this week
- A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-…☆119Updated this week
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆28Feb 19, 2026Updated 2 weeks ago
- SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organism…☆66May 5, 2023Updated 2 years ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆13Aug 26, 2024Updated last year
- ☆50Mar 11, 2022Updated 3 years ago
- InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..☆31Dec 27, 2023Updated 2 years ago
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.☆14May 12, 2024Updated last year
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year