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☆44Updated last year
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- TAXnomic Profile Aggregation and STAndardisation☆34Updated last week
- ☆33Updated 2 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆28Updated 6 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆23Updated 6 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 7 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆29Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆22Updated last month
- Predict plasmids from uncorrected long read data☆39Updated 4 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆24Updated 2 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆25Updated last month
- Gene-flank analysis tool☆26Updated 6 months ago
- strain-level analysis tools☆33Updated 2 weeks ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 2 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated last month
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆46Updated 2 years ago
- Long read metagenomics practical at EBAME18☆18Updated 6 years ago
- Intra-species bacterial contamination detection☆22Updated last year
- Recombination-free trees☆56Updated last year
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆18Updated 2 years ago
- Annotate your metagenome assemblies☆11Updated 6 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆26Updated 4 months ago
- A toolkit for prokaryotic comparative genomics☆25Updated 2 months ago
- Phylogeny Enhanded Prediction of PAN-genome☆39Updated 4 years ago