theiagen / public_health_viral_genomics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
☆41Updated 3 months ago
Related projects ⓘ
Alternatives and complementary repositories for public_health_viral_genomics
- ☆27Updated last year
- Primer schemes for real-time genome epidemiology☆27Updated last year
- Split Kmer Analysis☆63Updated 2 years ago
- UPHL's Reference Free Pipeline☆25Updated 2 weeks ago
- Influenza genome analysis Nextflow workflow☆22Updated 3 weeks ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆27Updated 4 months ago
- Recombination-free trees☆56Updated last year
- SC2 variant detection and composition pipeline☆16Updated last year
- InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..☆30Updated 10 months ago
- Reference-based consensus creation☆50Updated this week
- Fast k-mer based tool for multi locus sequence typing (MLST)☆42Updated 4 years ago
- Basic workflow for nanopore sequencing data☆14Updated 2 weeks ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆29Updated last month
- de novo virus assembler of Illumina paired reads☆54Updated 3 years ago
- Bioinformatics Pipeline and Visualization resources☆54Updated 2 months ago
- MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…☆41Updated 3 months ago
- whole genome MLST analysis☆38Updated 6 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆25Updated last month
- ☆44Updated 2 weeks ago
- Influenza genome analysis Nextflow workflow☆17Updated 3 weeks ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated last year
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 3 years ago
- IS mapping software☆51Updated 2 years ago
- Predict plasmids from uncorrected long read data☆39Updated 4 years ago
- Code Safety Inspection Service☆20Updated 2 years ago
- tools for assessing the accuracy of genome assemblies☆34Updated 7 months ago
- Standard database for the TBProfiler tool☆29Updated last month
- ☆34Updated 2 years ago
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago