cvn001 / transflow
A snakemake workflow for WGS-based tuberculosis transmission analysis
☆15Updated last month
Alternatives and similar repositories for transflow:
Users that are interested in transflow are comparing it to the libraries listed below
- Targeted Detection and Reconstruction of Plasmids☆20Updated 8 months ago
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆22Updated this week
- Hierarchical clustering of cgMLST☆11Updated last year
- Various scripts for efficient processing of 10k Salmonella genomes☆14Updated 3 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated last year
- A simple-to-use tool for visualizing and comparing genome contexts for numerous genomes☆15Updated 7 months ago
- Microbial Genome Circular plotting tool for comparative genomics using Circos☆37Updated last year
- whole genome MLST analysis☆40Updated 8 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆55Updated last week
- IslandPath standalone software☆31Updated last year
- In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outb…☆3Updated 3 months ago
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- Phasing for metagenomics using PacBio long reads☆17Updated 3 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆40Updated 4 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆30Updated last month
- Infer transmission clusters from SNP and timing data☆13Updated 4 years ago
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆23Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files☆20Updated last year
- A pipeline to investigate horizontal gene transfer from NGS data☆24Updated this week
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Identify phage regions in bacterial genomes for masking purposes☆30Updated 5 years ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆23Updated last year
- Microbial agile accurate SNP Typer☆29Updated last year
- A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research☆14Updated this week
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- Quality control plotting for long reads☆10Updated 8 months ago
- This repository contains R code for building a heatmap and histogram with the output of FastANI☆16Updated 3 years ago
- vSNP -- validate SNPs☆20Updated 4 months ago