Pathogen Informatics, Wellcome Sanger Institute

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

sanger-pathogens

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

sanger-pathogens

de novo virus assembler of Illumina paired reads

sanger-pathogens

Multilocus sequence typing by blast using the schemes from PubMLST

sanger-pathogens

Assembling the cause of phenotypes and genotypes from NGS data

sanger-pathogens

Python3 module for running MUMmer and reading the output

sanger-pathogens

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

sanger-pathogens

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

sanger-pathogens

Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment

sanger-pathogens