BU-ISCIII / bacterial_wgs_training
In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.
☆2Updated 3 weeks ago
Related projects ⓘ
Alternatives and complementary repositories for bacterial_wgs_training
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆22Updated last month
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆19Updated 5 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆23Updated 6 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated last year
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆24Updated 2 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Quality control plotting for long reads☆10Updated 6 months ago
- Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes☆15Updated 4 years ago
- whole genome MLST analysis☆38Updated 6 months ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆25Updated last month
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated this week
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 7 months ago
- Predict plasmids from uncorrected long read data☆39Updated 4 years ago
- ☆18Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 5 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆28Updated last year
- A pipeline for performing genome-wide association tests for bacterial genomes.☆28Updated 6 years ago
- Long read metagenomics practical at EBAME18☆18Updated 6 years ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 3 years ago
- UPHL's Reference Free Pipeline☆25Updated 2 weeks ago
- Intra-species bacterial contamination detection☆22Updated this week
- genomic alignment similarity search tool☆19Updated 5 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆28Updated 2 months ago
- Predict MLST directly from uncorrected long reads☆25Updated 2 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆13Updated last year
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Updated 6 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆29Updated last month