ukhsa-collaboration / PneumoCaTLinks
Pneumococcal Capsular Typing tool for NGS data
☆18Updated 4 years ago
Alternatives and similar repositories for PneumoCaT
Users that are interested in PneumoCaT are comparing it to the libraries listed below
Sorting:
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Intra-species bacterial contamination detection☆25Updated 7 months ago
- ☆24Updated 6 years ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 2 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Recombination-free trees☆60Updated 3 weeks ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆54Updated 5 months ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Updated 2 years ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆14Updated 7 months ago
- Colinear block visualisation tool☆31Updated last year
- Automated strain separation of low-complexity metagenomes☆50Updated 3 years ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated last month
- Interactive, web tool for exploring pan-genome of bacterial strains☆46Updated 2 years ago
- Genome size estimation from long read overlaps☆61Updated this week
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆26Updated 3 years ago
- Pipeline for analysing intergenic regions in bacteria☆40Updated 5 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆57Updated this week
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆62Updated 3 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆39Updated last month
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 6 months ago
- Resolving Species Level Classification Using Emu☆14Updated last year
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆31Updated 3 weeks ago