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
- SC2 variant detection and composition pipeline☆16Updated last year
- Fast k-mer based tool for multi locus sequence typing (MLST)☆42Updated 4 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated last year
- Primer schemes for real-time genome epidemiology☆27Updated last year
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆25Updated last month
- Split Kmer Analysis☆63Updated 2 years ago
- Influenza genome analysis Nextflow workflow☆22Updated last week
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆29Updated last month
- ☆51Updated 3 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 3 years ago
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆38Updated 3 years ago
- Visualize whole genome alignments as linear maps☆70Updated last month
- Influenza data pipeline to automate genotyping assignment☆21Updated 2 weeks ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆52Updated last year
- ☆44Updated this week
- Reference-based consensus creation☆50Updated this week
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- Harmonization of AMR predictor tool outputs☆21Updated last year
- IS mapping software☆51Updated 2 years ago
- Bioinformatics Pipeline and Visualization resources☆54Updated 2 months ago
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- de novo virus assembler of Illumina paired reads☆54Updated 3 years ago
- ☆26Updated 5 years ago
- whole genome MLST analysis☆38Updated 5 months ago
- Recombination-free trees☆56Updated last year
- tools for assessing the accuracy of genome assemblies☆34Updated 6 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
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Updated 2 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆92Updated this week