nf-core / pathogensurveillanceLinks
Surveillance of pathogens using population genomics and sequencing
☆43Updated 3 months ago
Alternatives and similar repositories for pathogensurveillance
Users that are interested in pathogensurveillance are comparing it to the libraries listed below
Sorting:
- Recombination-free trees☆60Updated last month
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Graph-based assembly phasing☆87Updated 5 months ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆62Updated last year
- ☆37Updated 3 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆41Updated this week
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆49Updated 3 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆66Updated 3 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆62Updated 3 months ago
- Gene-flank analysis tool☆30Updated 9 months ago
- Bacterial GWAS analysis☆43Updated 2 months ago
- Phylogeny Enhanded Prediction of PAN-genome☆42Updated 5 years ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆54Updated 3 months ago
- ☆53Updated 4 years ago
- BEAV: Bacterial Element Annotation reVamped☆69Updated last month
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆30Updated last week
- TAXnomic Profile Aggregation and STAndardisation☆41Updated last month
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated last year
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Bifrost graph gene caller.☆95Updated 2 weeks ago
- Long read metagenomics practical at EBAME18☆18Updated 7 years ago
- Microbial Genome Circular plotting tool for comparative genomics using Circos☆38Updated 2 years ago
- Collection of R scripts for SARS-CoV-2 (variant) analyses☆12Updated 2 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- tools for assessing the accuracy of genome assemblies☆34Updated last year
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆60Updated 2 weeks ago