lskatz / lyve-SETLinks
LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
☆27Updated 10 months ago
Alternatives and similar repositories for lyve-SET
Users that are interested in lyve-SET are comparing it to the libraries listed below
Sorting:
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- Recombination-free trees☆58Updated 3 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆36Updated 3 months ago
- reference-based long read assemblies of bacterial genomes☆50Updated 3 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated 2 years ago
- Order and orientation of complete bacterial genomes☆28Updated last week
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated this week
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated last month
- A tool for removing redundant genomes from a set of assemblies☆71Updated last year
- Split Kmer Analysis☆65Updated 3 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆38Updated last month
- Identify phage regions in bacterial genomes for masking purposes☆33Updated 5 years ago
- Intra-species bacterial contamination detection☆25Updated 5 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 3 months ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆26Updated 9 months ago
- List and download schemes from pubMLST.org and other BIGSDB servers☆10Updated 9 months ago
- ☆36Updated 3 months ago
- Clermont PCR method In-Silico☆22Updated last year
- CFSAN Shigella Typing Pipeline☆14Updated 2 years ago
- ☆53Updated 4 years ago
- all methods related to Enterobase☆42Updated 10 months ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆32Updated 2 months ago
- Bifrost graph gene caller.☆95Updated 9 months ago
- Plasmid analysis using rearrangement distances☆42Updated last month
- Fast k-mer based tool for multi locus sequence typing (MLST)☆46Updated 4 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 2 months ago
- UPHL's Reference Free Pipeline☆26Updated 2 weeks ago