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Pathogen Informatics, Wellcome Sanger Institute (sanger-pathogens)

Pathogen Informatics, Wellcome Sanger Institute

sanger-pathogens

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Location:Hinxton, Cambs., UK

Home Page:http://www.sanger.ac.uk/science/groups/pathogen-informatics

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Pathogen Informatics, Wellcome Sanger Institute's repositories

Roary

Rapid large-scale prokaryote pan genome analysis

Language:PerlLicense:NOASSERTIONStargazers:297Issues:28Issues:393

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

Language:JavaLicense:NOASSERTIONStargazers:227Issues:17Issues:61

circlator

A tool to circularize genome assemblies

Language:PythonLicense:NOASSERTIONStargazers:219Issues:21Issues:101

ariba

Antimicrobial Resistance Identification By Assembly

Language:PythonLicense:NOASSERTIONStargazers:155Issues:22Issues:120

assembly-stats

Get assembly statistics from FASTA and FASTQ files

Language:C++License:NOASSERTIONStargazers:108Issues:18Issues:5

mlst_check

Multilocus sequence typing by blast using the schemes from PubMLST

Language:PerlLicense:NOASSERTIONStargazers:27Issues:5Issues:13

pymummer

Python3 module for running MUMmer and reading the output

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Bio-Tradis

A set of tools to analyse the output from TraDIS analyses

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seroba

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

Language:PythonLicense:NOASSERTIONStargazers:16Issues:7Issues:39

vr-codebase

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

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nano-rave

Nextflow pipeline designed for rapid onsite QC and variant calling of Oxford Nanopore data (following basecalling and demultiplexing with Guppy).

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update_pipeline

Update a pipelines metadata

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Bio-InterProScanWrapper

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unix-training

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

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Bio-AutomatedAnnotation

Perl module to take in an genomic assembly and produce annoation

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Bio-ReferenceManager

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monocle

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nextflow-commons

Store of generic templates and scripts for nextflow pipelines

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paminfo-open-lab-event

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python_fun

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bactgen-training-app

Static site for training on the Juno/GPS2 projects

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bentley-app

Static site for Stephen Bentley's group

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Bio-Path-Find

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Bio-Track-Schema

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Bio-VertRes-Config

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external-import

Import external data into our tracking databases

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multimapper

Updated conversions of Simon Harris' pipelines

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paminfo-training-FE

A lightweight frontend application used for testing applicants

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software-tracker

API and helper scripts for the pathogen software installation tracking database

Language:PythonStargazers:0Issues:2Issues:1

TpRNAseq

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

Language:NextflowLicense:MITStargazers:0Issues:3Issues:0