lskatz / lyve-SETLinks
LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
☆27Updated last year
Alternatives and similar repositories for lyve-SET
Users that are interested in lyve-SET are comparing it to the libraries listed below
Sorting:
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆62Updated 3 months ago
- Recombination-free trees☆60Updated last month
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated last week
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Split Kmer Analysis☆65Updated 3 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆57Updated this week
- Bifrost graph gene caller.☆95Updated 2 weeks ago
- Intra-species bacterial contamination detection☆25Updated 7 months ago
- a collection of scripts for organising bacterial genomes by species☆77Updated 3 years ago
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- Identify phage regions in bacterial genomes for masking purposes☆34Updated 6 years ago
- Order and orientation of complete bacterial genomes☆28Updated 2 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 2 months ago
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 weeks ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆43Updated 6 months ago
- Automated strain separation of low-complexity metagenomes☆50Updated 3 years ago
- Clermont PCR method In-Silico☆23Updated last year
- SC2 variant detection and composition pipeline☆17Updated 2 years ago
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆55Updated 5 months ago
- ☆36Updated 5 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆41Updated last month
- Influenza data pipeline to automate genotyping assignment☆37Updated 4 months ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆34Updated 10 months ago
- REcombination BARcode detector.☆16Updated last year