sanger-pathogens Goto Github PK

paminfo-training-fe

A lightweight frontend application used for testing applicants

panito

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

panoptes

Eyes on your (genomic) data

pathfind-training

pathogen-informatics-training

pipelines_reporting

plasmidtron

Assembling the cause of phenotypes and genotypes from NGS data

pymummer

Python3 module for running MUMmer and reading the output

python_fun

qc-training

remove_blocks_from_aln

roary

Rapid large-scale prokaryote pan genome analysis

saffrontree

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

sanger-pathogens.github.io

Summary of Sanger Pathogen's Repos

seroba

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

setup_tracking

setup a vrtracking pipeline

singularity-bsub

Provides wrapper scripts for executing LSF commands within a Singularity container

snp-sites

Finds SNP sites from a multi-FASTA alignment file

snpeffwrapper

Takes a VCF and applies annotations from a GFF using SnpEff

software-tracker

API and helper scripts for the pathogen software installation tracking database

spn-resistance_sanger

Resistance pipeline for Sanger Cluster

tprnaseq

A bacterial RNAseq pipeline, designed for analysis of Treponema pallidum data

unix-training

A set of jupyter notebooks to provide unix training developed by Pathogen Informatics at Wellcome Sanger Institute.

update_pipeline

Update a pipelines metadata

vr-codebase

The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute

writedb_entry_set

Repo to hold the writedb_entry_set Python code extracted from the Pathogen Informatics general GitLab repo.