lskatz / pdtk
NCBI Pathogen Detection Portal toolkit
☆11Updated last year
Related projects ⓘ
Alternatives and complementary repositories for pdtk
- CFSAN Shigella Typing Pipeline☆14Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 4 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- µbinfie blog☆16Updated 3 weeks ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆39Updated this week
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆11Updated 5 months ago
- Intra-species bacterial contamination detection☆22Updated this week
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆23Updated last month
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆19Updated 5 years ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆11Updated last year
- Visualize microbial evolution at the SNP level!☆13Updated last week
- Strain-level haplotyping for metagenomes with short or long-reads.☆41Updated 4 months ago
- Colinear block visualisation tool☆30Updated 10 months ago
- Predict MLST directly from uncorrected long reads☆25Updated 2 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Fast viral consensus genome reconstruction☆22Updated 4 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 7 months ago
- ☆19Updated last week
- Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria☆14Updated 3 years ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆11Updated 2 months ago
- software to identify primers that can distinguish genomes☆20Updated 3 weeks ago
- Plasmid analysis using rearrangement distances☆30Updated last week
- Organism-specific interpretation of AMR genotypes☆9Updated 8 months ago
- emm Automatic Isolate Labeller☆10Updated 2 months ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- UPHL's Reference Free Pipeline☆25Updated 2 weeks ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆11Updated last year
- Plasmid exploration of bacterial genomes☆17Updated 2 years ago