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Keyword
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- High-throughput sequencing35
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- DNA-Seq34
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Operation
- Allele calling3
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- Exome variant detection3
- Functional genome annotation3
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- Consensus-based sequence alignment2
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- Breakend assembly1
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- Genome assembly1
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Venue
- European Molecular Biology Laboratory11
- European Bioinformatics Institute, Hinxton10
- Craik-Marshall Building7
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- LANGEBIO, Cinvestav, Libramiento Norte Carretera Leon Km 9.62
- Online2
- The Revere Hotel2
- The workshop will take place at the Institute of Plant Molecular Biology building at the Academy of Sciences and University campus in České Budějovice, Branisovska 31, Czech Republic (http://goo.gl/maps/G74MI).2
- University of Ljubljana, Faculty of Medicine2
- 500 Hotel Circle North1
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- Birmingham Metabolomics Training Centre1
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- Rikli Balance Hotel, Cankarjeva cesta 4, SI-4260 Bled, Slovenia1
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- University of Maryland1
- University of Milano-Bicocca, Building U7, Lab 7151
- Università di Pavia, via Ferrata 11
- Via Pietro Castellino, 1111
- Wageningen University1
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- https://singlecell-pilsen2022.zcu.cz/location.html1
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Sponsor
- ELIXIR Europe3
- ABRomics2
- Aviesan ITMO GGB2
- ELIXIR EXCELERATE2
- IFB2
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- Institut Français de Bioinformatique2
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- INTERREG V-A Italy-Slovenia 2014-2020 project TRAIN1
- IRCCS Ospedale San Raffaele1
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- LINQ management GmbH1
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- Merck1
- NBIS - National Bioinformatics Infrastructure Sweden1
- NORBIS1
- National Research Council of Italy1
- Pan-Africa network for genomic surveillance of poverty related diseases and emerging pathogens1
- Pan-African Consortium for the Evaluation of Antituberculosis Antibiotics1
- South African National Bioinformatics Institute, University of the Western Cape1
- Swiss Tropical and Public Health Institute1
- The European & Developing Countries Clinical Trials Partnership1
- The European Union1
- The Foundation for Innovative New Diagnostics1
- Università Vita-Salute San Raffaele1
- VEIS1
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Target audience
- Researchers13
- PhD students11
- Graduate students8
- Institutions and other external Institutions or individuals7
- Postdocs and Staff members from the University of Cambridge7
- life scientists7
- This course is aimed at advanced PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing technologies in cancer research and wish to familiarise themselves with bioinformatics tools and data analysis methodologies specific to cancer data. Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor (basic understanding of the R syntax and ability to manipulate R objects) and the Unix/Linux operating system.3
- bioinformaticians3
- Cette formation est destinée aux biologistes (ingénieurs, doctorants, chercheurs, enseignants-chercheurs, praticiens…) confrontés à l’analyse de données NGS, et qui ne disposent pas des compétences bioinformatiques suffisantes.2
- Life Science Researchers2
- Master students2
- Postdoctoral Researchers2
- The course is aimed primarily at mid-career scientists – especially those whose formal education likely included statistics2
- but who have not perhaps put this into practice since.2
- Anyone intersted in GWAS and using the H3Africa genotyping chip1
- Beginners1
- Biologists1
- Biologists, Genomicists, Computer Scientists1
- Biotechnology Companies1
- Business Entrepreneurs1
- Clinicians1
- Cloud users1
- Companies 1
- Computational biologists1
- Developers1
- Este curso introductorio está destinado principalmente a becaries doctorales de iniciación, que buscan dar sus primeros pasos en el uso de R para análisis de datos genómicos. El curso está dirigido únicamente a académicos de países de América Latina, excluyendo a Chile y Uruguay por restricciones de financiamiento. Prerrequisitos No es necesario tener conocimiento previo o experiencia en línea de comandos. Se valorarán los conocimientos de biología molecular. Dado que la modalidad de cursada será virtual (sincrónica/ asincrónica) cada uno debe contar con acceso a PC y conexión a internet estable. No se requiere la instalación de programas, ya que se proveerá acceso a herramientas virtuales (ejemplo: RStudio virtual). Tenga en cuenta que este curso se impartirá en español, aunque los formadores dominan el inglés y pueden ofrecer apoyo lingüístico cuando sea posible. Se dará prioridad en la inscripción a estudiantes de doctorado de iniciación. Alentamos la postulación de todes les becaries de grupos subrepresentados a este taller. Se dará prioridad de asistencia a aquellos que aún no hayan asistido a un evento de CABANA.1
- Galaxy users1
- HPC users1
- PhD candidates1
- Pharmaceutical Industry1
- Post Docs1
- Postgraduate students1
- Researcher in life sciences1
- The course is suitable for graduate students and young researchers with a background in biology who are keen to become proficient bioinformaticians within the fields of genomics and/or transcriptomics. We will start with the basics, so students with no prior programming knowledge are welcome. We have a number of Linux computers that you can use, and you can bring your own laptops*. Please note this course will be taught in English, however the trainers are fluent in either Spanish or Portuguese, and can offer language support where feasible. A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form. *If you bring your own laptop (any operating system is fine), you must have installed the following programs: R (at least version 3.5), the latest Rstudio and Bioconductor. To download R please visit: https://www.r-project.org/ To download RStudio please visit: https://www.rstudio.com/products/rstudio/download/ Bioconductor must be downloaded and installed via R, instructions on how to do this can be found here: https://www.bioconductor.org/install/1
- The handson component is aimed at novice to intermediate users who are seeking detailed guidance with GATK and related tools.1
- The lecture based component of the workshop is aimed at a mixed audience of people who are new to the topic of variant discovery or to GATK1
- The primary target audience is researchers working in FAANG projects, including AQUA-FAANG, GENE-SWitCH and BovReg. Familiarity with running bioinformatic analysis of sequencing data in a Unix environment is essential for those attending this training.1
- This course is aimed at PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing technologies in cancer research and wish to familiarise themselves with bioinformatics tools and data analysis methodologies specific to cancer data. Familiarity with the technology and biological use cases of high throughput sequencing (HTS) is required, as is some experience with R/Bioconductor (basic understanding of the R syntax and ability to manipulate R objects) and the Unix/Linux operating system.1
- This course is aimed at PhD students and post-doctoral researchers who are using high-throughput sequencing technologies and bioinformatics methods in their research. The content is most applicable for those working with eukaryotic genomes, human genetics and in rare disease research. Participants will require a basic knowledge of the Unix command line, the Ubuntu 16 operating system and the R statistical packages. We recommend these free tutorials: Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training Basic R concept tutorials: www.r-tutor.com/r-introduction Please note: participants without basic knowledge of these resources will have difficulty in completing the practical sessions.1
- This course is aimed at PhD students and postdoctoral researchers needing to learn about methods and approaches for manipulating and analysing livestock genomic data. It will help those wanting to start basic identification of genetic variation, annotating function to genomic data, and using public data to interpret new findings. Participants will require a basic knowledge of the Unix command line, the Ubuntu 18 operating system and the R statistical packages. We recommend these free tutorials: Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training Basic R concept tutorials: www.r-tutor.com/r-introduction Regardless of your current knowledge we encourage successful participants to use these, and other materials, to prepare for attending the course and future work in this area. 1
- This course is aimed at researchers at any career stage within the University of Pavia and Institute of Molecular Genetics who are working with and/or generating their own genomic and biomolecular datasets. No knowledge of programming is required, but an undergraduate level knowledge of Biology / molecular biology would be beneficial.1
- This course is aimed at researchers at graduate level upwards within Latin America who are working with and/or generating their own crop genomic data or who are working on genotyping technologies, including data analysis software development. Prerequisites: Basic computational or previous bioinformatics experience is required for this workshop, such as basic commands in R. Undergraduate-level knowledge of plant biology would be an advantage. Please note this course will be taught in English. There will be assistants fluent in Spanish who can offer language support where feasible.1
- This course is aimed at researchers from postgraduate level upwards interested in using R to analyse genomics data for crop biodiversity studies. Please note this course will be taught in English, however the trainers are fluent in Spanish, and can offer language support where feasible. A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form. Prerequisites An undergraduate level degree in plant biology or a related discipline would be an advantage. You will need to know basic commands in R in order to get the most from this course, though a review of basic concepts and commands in R will be covered on the first day. You can find a good introduction to R here: http://www.r-tutor.com/r-introduction You will also need to bring a laptop with R installed and working knowledge of how to navigate your working directory effectively using R commands. To download R please visit: https://www.r-project.org/ To download RStudio please visit: https://www.rstudio.com/products/rstudio/download/1
- This course is aimed at wet-lab researchers at any career stage within Latin America undertaking pathogen population genetics and surveillance, interested in applying next generation sequencing to virus identification. Those working in plant protection organizations and/or academia are welcome to apply, and priority will be given to those who have not yet attended a CABANA workshop. Please note this course will be taught in English, however the trainers are fluent in Spanish, and can offer language support where feasible. A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form. Priority will be given to those who have not previously been awarded a CABANA fellowship. Knowledge in R and NGS technologies is required. Therefore, these free resources should be studied beforehand: Basic R concept tutorials: www.r-tutor.com/r-introduction https://r4ds.had.co.nz/tidy-data.html Learning outcomes1
- This course is intended for PhD students of Portuguese and international institutions (with a particular focus on students of the CIBIO-InBIO’s BIODIV, SUSFOR Doctoral Programs and University of Porto), but more experienced researchers that are initiating projects in the field of environmental metagenomics can also participate. Prerequisite knowledge No previous bioinformatics experience is required, but an undergraduate level understanding of biology would be an advantage.1
- This course is suitable for all users who have an interest in Clinical Genetics with a special emphasis on rare disorders. It is also pertinent to those who seek to develop a better understanding of the role of accurate phenotyping in aiding the interpretation of filtered variants in patients and understanding genotype-phenotype correlations.1
- This workshop is aimed at PhD students within the PhD programme "Genetics, Molecular and Cellular Biology" (University of Pavia) and the PhD programmme "Biomolecular Sciences and Biotechnology" (IUSS, University School for Advanced Studies Pavia. No knowledge of programming is required, but an undergraduate level knowledge of biology or molecular biology would be useful.1
- Wet-lab researchers and bioinformaticians1
- beginner bioinformaticians1
- evolutionary biologists who already have bioinformatics skills. PhD students and Post-Doc researchers will benefit the most out of this course, but applications from all candidates will be evaluated in their context1
- or who are already GATK users seeking to improve their understanding of and proficiency with the tools.1
- post-docs1
- post-doctoral researchers and principle investigators working in wet-lab biology. Participants who are looking for a basic introduction to the bioinformatics resources offered by the EMBL-EBI and want to know more about accessing biological data and tools.1
- postdoc1
- postdocs.1
- seeking an introductory course into the tools1
- software developers, bioinformaticians1
- software engineers1
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