OLC-Bioinformatics / ConFindrLinks
Intra-species bacterial contamination detection
☆25Updated 6 months ago
Alternatives and similar repositories for ConFindr
Users that are interested in ConFindr are comparing it to the libraries listed below
Sorting:
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated 2 weeks ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆46Updated 2 years ago
- CFSAN Shigella Typing Pipeline☆14Updated 2 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆27Updated last month
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Order and orientation of complete bacterial genomes☆28Updated last month
- Recombination-free trees☆59Updated 5 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- reference-based long read assemblies of bacterial genomes☆50Updated 4 years ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆19Updated 2 years ago
- Bacterial genomes finishing tool for structural insights on draft genomes☆24Updated last year
- A taxonomic classifier of plasmids☆27Updated 4 years ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆49Updated last month
- Colinear block visualisation tool☆31Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Updated 4 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆49Updated 2 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆60Updated 2 months ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 5 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆26Updated 3 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- MAG Circularization Method☆33Updated 3 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆37Updated 2 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- frame-shift correction for long-read (meta)genomics☆34Updated last year