lskatz / lyve-SET
LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
☆25Updated 2 months ago
Related projects ⓘ
Alternatives and complementary repositories for lyve-SET
- Recombination-free trees☆56Updated last year
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated last year
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- Predict MLST directly from uncorrected long reads☆25Updated 2 years ago
- Split Kmer Analysis☆63Updated 2 years ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- UPHL's Reference Free Pipeline☆25Updated 2 weeks ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆25Updated last month
- ☆19Updated last week
- Basic workflow for nanopore sequencing data☆14Updated 2 weeks ago
- Code Safety Inspection Service☆20Updated 2 years ago
- Order and orientation of complete bacterial genomes☆27Updated 11 months ago
- post processing of bacterial pangenome gene presence/absence matrices☆52Updated 2 months ago
- Influenza data pipeline to automate genotyping assignment☆22Updated 3 weeks ago
- Predict plasmids from uncorrected long read data☆39Updated 4 years ago
- A tool for removing redundant genomes from a set of assemblies☆68Updated last year
- Identify phage regions in bacterial genomes for masking purposes☆30Updated 5 years ago
- CDCgov/mycosnp-nf☆37Updated 2 months ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆46Updated 2 years ago
- a collection of scripts for organising bacterial genomes by species☆76Updated 2 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 weeks ago
- SC2 variant detection and composition pipeline☆16Updated last year
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated 7 months ago
- ☆44Updated 2 weeks ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆29Updated last month
- SeqSero2☆33Updated 7 months ago
- ☆34Updated 2 years ago
- A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing☆39Updated 3 months ago
- REcombination BARcode detector.☆13Updated 7 months ago