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sanger-pathogens.github.io

Pathogen Informatics Repos

Wellcome Trust Sanger Institute. A list of our favorite repos from Pathogen Informatics. Rapid large-scale prokaryote pan genome analysis. Latest Release: v3.6.6. 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. A tool to circularize genome assemblies. Latest Release: v1.3.0. Antibiotic Resistance Identification By Assembly. Rapid annotation transfer tool. A wor...

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Pathogen Informatics Repos | sanger-pathogens.github.io Reviews
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Wellcome Trust Sanger Institute. A list of our favorite repos from Pathogen Informatics. Rapid large-scale prokaryote pan genome analysis. Latest Release: v3.6.6. 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. A tool to circularize genome assemblies. Latest Release: v1.3.0. Antibiotic Resistance Identification By Assembly. Rapid annotation transfer tool. A wor...
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1 pathogen informatics
2 featured repos
3 roary
4 artemis
5 circlator
6 other repos
7 repository
8 score
9 ariba
10 gubbins
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Pathogen Informatics Repos | sanger-pathogens.github.io Reviews

https://sanger-pathogens.github.io

Wellcome Trust Sanger Institute. A list of our favorite repos from Pathogen Informatics. Rapid large-scale prokaryote pan genome analysis. Latest Release: v3.6.6. 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. A tool to circularize genome assemblies. Latest Release: v1.3.0. Antibiotic Resistance Identification By Assembly. Rapid annotation transfer tool. A wor...

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sanger-pathogens.github.io sanger-pathogens.github.io
1

IVA

http://sanger-pathogens.github.io/iva

Download this project as a .zip file. Download this project as a tar.gz file. Assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth. For more information, please read the IVA publication. Installation instructions are below. For usage help and examples, see the IVA wiki page. IVA is installed on the Sanger pathogens virtual machine. Version 3.3 or higher (IVA is written in Python 3).

2

Gubbins - Genealogies Unbiased By recomBinations In Nucleotide Sequences

http://sanger-pathogens.github.io/gubbins

View source code on GitHub. Genealogies Unbiased By recomBinations In Nucleotide Sequences. Download source code as a .zip file. Download source code as a tar.gz file. The paper is available from Nucleic Acids Research (open access): Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R. Data used in the paper. Email gubbins@sanger.ac.uk. The a...

3

Pathogens-vm

http://sanger-pathogens.github.io/pathogens-vm

A virtual machine with Sanger pathogens software installed. A virtual machine made by the Pathogen Informatics team of the Sanger Institute, which includes the following software developed by the Pathogens group. The virtual machine is based on Bio-Linux. And so it also includes all the software that comes with Bio-Linux. How to get and use the virtual machine. Download the latest virtual machine. Or browse the directory of older versions. Start VirtualBox and choose File - Import Appliance from the menu.

4

Circlator

http://sanger-pathogens.github.io/circlator

A tool to circularize genome assemblies. A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0. PMID: 26714481. For how to use Circlator, please see the Circlator wiki page. Using pip or from source. Version = 0.7.12. Version = 2.6. Version = 3.23. Li, H et al....

5

Roary: the pan genome pipeline

http://sanger-pathogens.github.io/Roary

Roary: the Pan Genome Pipeline. By Andrew Page based on version 3.6.1 (19-April-2016). Citation and further details of the method. Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015;31(22):3691-3693 doi:10.1093/bioinformatics/btv421. Step by step tutorial. Details on how to install Roary. Input files from Prokka.

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Pathogen Informatics Repos

Wellcome Trust Sanger Institute. A list of our favorite repos from Pathogen Informatics. Rapid large-scale prokaryote pan genome analysis. Latest Release: v3.6.6. 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. A tool to circularize genome assemblies. Latest Release: v1.3.0. Antibiotic Resistance Identification By Assembly. Rapid annotation transfer tool. A wor...

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Home page - Wellcome Trust Sanger Institute

Clean water most effective against dysentery bacteria. Bacterial genomics and evolution. Image: Wellcome Library, London]. Bacteria provides insight into HIV and TB. Horse pathogen sheds light on persistent infections. Image: Wellcome Library, London]. EUMODIC studies over 300 mouse genes. Major study reveals role of genes in disease. Mouse and Zebrafish Laboratory. Image: Wellcome Library, London]. Last modified: Tue, 17 Mar 2015 12:43:45 GMT.

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