lskatz / pdtk
NCBI Pathogen Detection Portal toolkit
☆11Updated last year
Alternatives and similar repositories for pdtk:
Users that are interested in pdtk are comparing it to the libraries listed below
- CFSAN Shigella Typing Pipeline☆14Updated last year
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 7 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 4 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- µbinfie blog☆17Updated this week
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆12Updated 2 weeks ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆11Updated 8 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 10 months ago
- Visualize microbial evolution at the SNP level!☆14Updated 3 months ago
- Genome size estimation from long read overlaps☆48Updated 2 months ago
- Intra-species bacterial contamination detection☆25Updated last week
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆11Updated last year
- software to identify primers that can distinguish genomes☆21Updated 3 weeks ago
- ☆10Updated 2 months ago
- Predict MLST directly from uncorrected long reads☆27Updated 2 years ago
- Fast viral consensus genome reconstruction☆22Updated 2 months ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆11Updated 5 months ago
- Organism-specific interpretation of AMR genotypes☆10Updated 11 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated 3 weeks ago
- Colinear block visualisation tool☆30Updated last year
- Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria☆14Updated 3 years ago
- Disty McMatrixface - compute a distance matrix from a core genome alignment file☆14Updated last year
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 7 months ago
- Generate basic stats for an assembly.☆10Updated 2 years ago
- REcombination BARcode detector.☆13Updated 10 months ago
- ☆18Updated last month
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Plasmid analysis using rearrangement distances☆31Updated 3 months ago