typhoidgenomics / genotyphi
Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
☆24Updated 6 months ago
Alternatives and similar repositories for genotyphi:
Users that are interested in genotyphi are comparing it to the libraries listed below
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆20Updated this week
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- Intra-species bacterial contamination detection☆25Updated last month
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆33Updated last week
- A script for comparing old vs new versions of genome annotations☆20Updated last year
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Long read metagenomics practical at EBAME18☆18Updated 6 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 8 months ago
- Genome size estimation from long read overlaps☆51Updated 3 months ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆23Updated 6 years ago
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Updated 2 years ago
- Recombination-free trees☆57Updated last week
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆57Updated 3 weeks ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Colinear block visualisation tool☆30Updated last year
- frame-shift correction for long-read (meta)genomics☆33Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆20Updated 2 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated 11 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 4 years ago
- Plasmid exploration of bacterial genomes☆18Updated 3 years ago
- Remove human reads from a sequencing run☆38Updated 6 months ago