typhoidgenomics / genotyphiLinks
Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
☆28Updated 4 months ago
Alternatives and similar repositories for genotyphi
Users that are interested in genotyphi are comparing it to the libraries listed below
Sorting:
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- Predict MLST directly from uncorrected long reads☆27Updated 2 weeks ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Intra-species bacterial contamination detection☆25Updated 9 months 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
- Colinear block visualisation tool☆31Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆56Updated 7 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 5 months ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Predict plasmids from uncorrected long read data☆41Updated 2 weeks ago
- Order and orientation of complete bacterial genomes☆29Updated 4 months ago
- frame-shift correction for long-read (meta)genomics☆33Updated last year
- Microbial agile accurate SNP Typer☆29Updated last year
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Updated 2 years ago
- Recombination-free trees☆60Updated 2 months ago
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆27Updated last month
- Automated strain separation of low-complexity metagenomes☆52Updated 4 years ago
- Plasmid analysis using rearrangement distances☆46Updated 2 months ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Updated 3 years ago
- Whole genome core alignments from multiple draft genomes☆13Updated 9 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Updated 3 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- ☆23Updated this week