Pinned Repositories
ariba
Antimicrobial Resistance Identification By Assembly
Artemis
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
assembly-stats
Get assembly statistics from FASTA and FASTQ files
assembly_improvement
Improve the quality of a denovo assembly by scaffolding and gap filling
circlator
A tool to circularize genome assemblies
Fastaq
Python3 scripts to manipulate FASTA and FASTQ files
iva
de novo virus assembler of Illumina paired reads
pathogen-informatics-training
Roary
Rapid large-scale prokaryote pan genome analysis
snp-sites
Finds SNP sites from a multi-FASTA alignment file
Pathogen Informatics, Wellcome Sanger Institute's Repositories
sanger-pathogens/Artemis
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
sanger-pathogens/circlator
A tool to circularize genome assemblies
sanger-pathogens/ariba
Antimicrobial Resistance Identification By Assembly
sanger-pathogens/assembly-stats
Get assembly statistics from FASTA and FASTQ files
sanger-pathogens/Bio-Tradis
A set of tools to analyse the output from TraDIS analyses
sanger-pathogens/seroba
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
sanger-pathogens/vr-codebase
The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute
sanger-pathogens/nano-rave
Nextflow pipeline designed for rapid onsite QC and variant calling of Oxford Nanopore data (following basecalling and demultiplexing with Guppy).
sanger-pathogens/Bio-InterProScanWrapper
sanger-pathogens/Bio-AutomatedAnnotation
Perl module to take in an genomic assembly and produce annoation
sanger-pathogens/Bio-ReferenceManager
sanger-pathogens/long-read-ampliseq
sanger-pathogens/monocle
sanger-pathogens/nextflow-commons
Store of generic templates and scripts for nextflow pipelines
sanger-pathogens/paminfo-open-lab-event
sanger-pathogens/python_fun
sanger-pathogens/bactgen-training-app
Static site for training on the Juno/GPS2 projects
sanger-pathogens/bentley-app
Static site for Stephen Bentley's group
sanger-pathogens/assorted-sub-workflows
sanger-pathogens/Bio-Path-Find
sanger-pathogens/Bio-Track-Schema
sanger-pathogens/Bio-VertRes-Config
sanger-pathogens/external-import
Import external data into our tracking databases
sanger-pathogens/multimapper
Updated conversions of Simon Harris' pipelines
sanger-pathogens/Multiple-mappings-to-bam
A GSoC project - Nextflow pipeline updating the legacy Python2 Multiple mappings to bam to nextflow.
sanger-pathogens/nextflowtool
sanger-pathogens/paminfo-training-FE
A lightweight frontend application used for testing applicants
sanger-pathogens/sh16_scripts
Deprecated scripts for reference only
sanger-pathogens/software-tracker
API and helper scripts for the pathogen software installation tracking database
sanger-pathogens/TpRNAseq
A bacterial RNAseq pipeline, designed for analysis of Treponema pallidum data