nf-core / pathogensurveillanceLinks
Surveillance of pathogens using population genomics and sequencing
☆43Updated 2 months ago
Alternatives and similar repositories for pathogensurveillance
Users that are interested in pathogensurveillance are comparing it to the libraries listed below
Sorting:
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆49Updated 2 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆61Updated 3 months ago
- Recombination-free trees☆60Updated 2 weeks ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆30Updated 10 months ago
- Split Kmer Analysis☆65Updated 3 years ago
- reference-based long read assemblies of bacterial genomes☆50Updated 4 years ago
- Graph-based assembly phasing☆87Updated 4 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- Ley Lab MetaGenome Profiler DataBase generator☆49Updated 2 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆66Updated 2 years ago
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆58Updated last year
- Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads☆28Updated last month
- Microbial Genome Circular plotting tool for comparative genomics using Circos☆38Updated 2 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 6 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆41Updated 4 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆42Updated 5 years ago
- Gene-flank analysis tool☆30Updated 9 months ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆46Updated 2 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆38Updated 3 months ago
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆60Updated 2 months ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆61Updated last year
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆37Updated this week
- ☆37Updated 3 years ago
- Metagenomic Analysis in Real Time☆28Updated last week
- A tool for removing redundant genomes from a set of assemblies☆76Updated last week
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆32Updated last month
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago