lskatz / pdtkLinks
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
Sorting:
- CFSAN Shigella Typing Pipeline☆14Updated 2 years ago
- A tool to detect acquired AMR genes directly from long read sequencing data.☆16Updated this week
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- Visualize microbial evolution at the SNP level!☆15Updated 2 months ago
- µbinfie blog☆17Updated 4 months ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Updated 5 months ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆11Updated last year
- A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…☆16Updated 9 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 3 months ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Updated 2 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated last month
- Organism-specific interpretation of AMR genotypes☆13Updated last year
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated this week
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆26Updated 9 months ago
- Colinear block visualisation tool☆31Updated last year
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- Intra-species bacterial contamination detection☆25Updated 5 months ago
- Genome size estimation from long read overlaps☆58Updated last week
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆24Updated 11 months ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 4 months ago
- Fast viral consensus genome reconstruction☆23Updated last week
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆11Updated 3 weeks ago
- software to identify primers that can distinguish genomes☆21Updated 5 months ago
- ☆20Updated 3 weeks ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- Bacterial surveillance pipeline.☆24Updated last month
- Resolving Species Level Classification Using Emu☆13Updated last year