tseemann / ekidna
Assembly based core genome SNP alignments for bacteria
☆25Updated 5 years ago
Related projects ⓘ
Alternatives and complementary repositories for ekidna
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 5 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated last year
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Predict plasmids from uncorrected long read data☆39Updated 4 years ago
- Intra-species bacterial contamination detection☆22Updated this week
- Recombination-free trees☆56Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆22Updated last month
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- Gene-flank analysis tool☆26Updated 6 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆24Updated 2 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆46Updated 2 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆23Updated 6 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated this week
- A pipeline for performing genome-wide association tests for bacterial genomes.☆28Updated 6 years ago
- TAXnomic Profile Aggregation and STAndardisation☆34Updated 3 weeks ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 7 months ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 7 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆19Updated 5 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆25Updated last week
- Colinear block visualisation tool☆30Updated 10 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated last year
- Split Kmer Analysis☆63Updated 2 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆28Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 4 months ago
- Bacterial genomes finishing tool for structural insights on draft genomes☆24Updated last year