Computational Resources In Infectious Disease
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This document summarizes bioinformatics tools that can be used for analysis of high-throughput sequencing data for molecular diagnostics. It discusses databases for virulence factors and antimicrobial resistance as well as tools for assembly, annotation, pan-genome analysis, visualization, and commercial solutions. The presentation emphasizes that there is no single best tool and different approaches are needed for different questions. Collaboration with other researchers is recommended.
Computational Resources In Infectious Disease
- 1. João André Carriço, Microbiology Institute and Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon [email protected] twitter: @jacarrico ME081 – Meet-The-Expert Session 26th ECCMID, Amsterdam, Netherlands 7-12 April 2016
- 2. This presentation is not intended to cover all available software or databases (we would need several weeks or months to do that) I’ll present what I use or intend to use in a near future I gladly accept any suggestions to included on similar presentations in the future. It is supposed to be interactive so ask away during the presentation.
- 3. Available Databases Virulence Factors and AMR DBs Sequence-based typing databases: Pubmlst.org / Enterobase HighThroughput Sequencing data analysis (freeware) Prokka Roary Nullabor Microreact.org PHYLOViZ Commercial Solutions Bionumerics 7.5 CLC GenomicsWorkbench (CLC Bio) Ridom Seqsphere+
- 4. Virulence Factor Databases VFDB (http://www.mgc.ac.cn/VFs/main.htm) Pathosystems Resource Integration Center (PATRIC) VF (https)://www.patricbrc.org/) Victors (http://www.phidias.us/victors/) PHI-Base (http://www.phi-base.org/) MvirDB (http://mvirdb.llnl.gov/ ) To know more: - Presentation on the Controversies in interpreting whole genome sequence data session : http://eccmidlive.org/#resources/how-can-we-design-actionable-virulome-databases
- 5. Comprehensive Antibiotic Resistance Database (CARD) (https://card.mcmaster.ca/) Repository of Antibiotic resistanceCassetes (RAC)(http://rac.aihi.mq.edu.au/rac/) Integrall :The integron database (http://integrall.bio.ua.pt/) (…)
- 6. To know more : http://www.slideshare.net/nickloman/eccmid-2015-so-i-have-sequenced-my-genome-what-now Reads (fastq files) contigs (fasta files) Annotated contigs (gbk/gff files) Roary :PanGenome Analysis Enterobase BIGSdb Nullabor PHYLOViZ: Tree + metada visualization Microreact.org: Tree +metadata +vizualization Prokka De novo assembler
- 8. slide by @happy_khan Martin Sergeant Mark Achtman Nabil-Fareed Alikhan Zhemin Zhou
- 9. Genome annotation made easy byTorsten Seemann (slides byTorsten) Genome annotation: adding biological information to the sequence, by describing features To know more : http://www.slideshare.net/torstenseemann/prokka-rapid-bacterial-genome-annotation-abphm-2013 Available at: https://github.com/tseemann/prokka
- 10. Pan genome analysis by Andrew Page Available at: https://sangerpathogens.github.io/Roary/ Core genome Accessory genome Pan-genome
- 11. Inputs:Annotated de novo assemblies (GFF files) • Typically from the annotation pipeline Outputs: • Spreadsheet with presence and absence of genes • Multi-FASTA alignment of core genes so you can build a tree without a reference • Multi-FASTA alignments for each gene • Plots for the open/closed genome, unique genes • Integrates with iCANDY so you can visualise all structural variation • QC report from Kraken to help identify suspect samples (Slide by Andrew Page)
- 12. Core (n or n-1 strains) Soft-Core (n-2 or n-3 strains) Shell ( 8(?) to n-3 strains) Cloud ( <8 (?) strains) Core genome: Core + Soft-Core Accessory genome: Shell + Cloud
- 13. iCANDY output of presence and absence of genes in accessory genome. S. Weltevreden & public S. enterica genomes (Slide by Andrew Page)
- 14. Complete pipeline from reads to reports byTorsten Seemann Objective is automate analysis for everyday use on public health labs /research settings Uses and distills outputs by a lot of software Avaliable at: https://github.com/tseemann/nullarbor
- 18. www.phyloviz.net
- 19. Inputs: - Tab separated txt (profiles) - Fasta files - Automatic database retrieval (MLST) Outputs: • goeBURST and goeBURST MST • Link quality assessment • High quality images Can be easily applied to: - MLST/ cgMLST/wgMLST - MLVA - SNP data* - Gene Presence/absence
- 20. New features: • Hierarchical clustering • Neighbor-Joining • Project Saving
- 21. Available at http://online.phyloviz.net Web based version of PHYLOViZ Allows users to create their own datasets, save them and share their data (privately or publicly) REST API available Scalable to thousands of nodes Tree Analysis tools: Interactive distance matrix NLV graph
- 24. NLV Graph Tree cut-off Full MST
- 27. Create Selections Change tree options
- 28. Available at http://microreact.org/ Presentation on session Harnessing whole genome sequence data for public health applications : Novel open access tools forWGS- based pathogen surveillance and the identification of high-risk clones http://eccmidlive.org/#resources/novel-open-access-tools-for- wgs-based-pathogen-surveillance-and-the-identification-of-high- risk-clones
- 30. • Ridom Seqsphere+ : http://www.ridom.de/seqsphere/ • Applied Maths Bionumerics 7.6: http://www.applied-maths.com/bionumerics • CLCBioGenomicWorkbench : http://www.clcbio.com/blog/clc-genomics-workbench-7-5/
- 31. • Huge variety of software and database solutions • There is no single One-Size-Fits-All solution (job security for bioinformaticians) • Different questions require different approaches • Always questions the results and data provenance
- 32. ECCMID2015 Meet-the-expert session on “What bioinformatic tools should I use for analysis of HighThroughput Sequencing data for molecular diagnostics? ” Nick Loman: http://www.slideshare.net/nickloman/eccmid-2015- meettheexpert-bioinformatics-tools João André Carriço: http://www.slideshare.net/joaoandrecarrico/eccmid-meet- theexpert2015
- 33. UMMI Members Bruno Gonçalves Mário Ramirez José Melo-Cristino INESC-ID Alexandre Francisco Cátia Vaz Marta Nascimento EFSA INNUENDO Project (https://sites.google.com/site/innuendocon/) Mirko Rossi FP7 PathoNGenTrace (http://www.patho-ngen-trace.eu/): Dag Harmsen (Univ. Muenster) Stefan Niemann (Research Center Borstel) Keith Jolley, James Bray and Martin Maiden (Univ. Oxford) Joerg Rothganger (RIDOM) Hannes Pouseele (Applied Maths) Genome Canada IRIDA project (www.irida.ca) Franklin Bristow, Thomas Matthews, Aaron Petkau, Morag Graham and Gary Van Domselaar(NLM , PHAC) Ed Taboada and Peter Kruczkiewicz (LabFoodborne Zoonoses, PHAC) Fiona Brinkman (SFU) William Hsiao (BCCDC) INTEGRATED RAPID INFECTIOUS DISEASE ANALYSIS