OLC-Bioinformatics / ConFindrLinks
Intra-species bacterial contamination detection
☆25Updated 9 months ago
Alternatives and similar repositories for ConFindr
Users that are interested in ConFindr are comparing it to the libraries listed below
Sorting:
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆31Updated this week
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Order and orientation of complete bacterial genomes☆29Updated 4 months ago
- Recombination-free trees☆60Updated 2 months ago
- Predict plasmids from uncorrected long read data☆41Updated 2 weeks ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 4 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- Bacterial genomes finishing tool for structural insights on draft genomes☆23Updated 2 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- Calculate assocations between genes and traits☆28Updated 8 months ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 8 months ago
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Updated 2 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Updated 3 years ago
- Colinear block visualisation tool☆31Updated last year
- Strain-level haplotyping for metagenomes with short or long-reads.☆56Updated 7 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆19Updated 2 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- PLSDB pipeline to collect bacterial plasmids from NCBI☆38Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Predict MLST directly from uncorrected long reads☆27Updated 2 weeks ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Updated 2 years ago
- frame-shift correction for long-read (meta)genomics☆33Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 5 months ago
- Get microbial sequence data easier and faster☆28Updated 6 years ago
- UPHL's Reference Free Pipeline☆27Updated 2 weeks ago