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Question: Links To Good Next Gen Sequence Analysis Training Courses And Centres
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Hi,

I am wondering if there is a good resource for staying aware of quality upcoming training events in NGS analysis. If no resource exists, I guess this thread could become one! I am based in the UK but training doesn't have to be local.

My particular interests would be in the areas of DNA/RNA-Seq, preferably with the more utilized open source tools.

Thanks in advance.

ADD COMMENTlink 8.5 years ago Travis ♦ 2.8k • updated 2.9 years ago carlopecoraro2 • 920
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Despite it is OK to ask this question here, its open question format is better suited for seqanswers. Then you can ask here close questions about specific courses or resources. I could be wrong but I see QA sites more effective when the forum questions type are in a very low proportion. Having said that I have found very useful the links in the answers and probably I would have miss them in the seqanswers sea of entries ;-)

ADD REPLYlink 8.5 years ago
Pablo Marin-Garcia
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Hi..We, Bionivid Technology in India are providing NGS Data Analysis learning program...Its a 5-days hands on training program whch includes both DNA and RNA seq data analysis training..for more info please visit http://www.bionivid.com/learning.html

ADD REPLYlink 7.6 years ago
Hitesh Goswami
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This BioStars post seem relevant: https://www.biostars.org/p/79845/

ADD REPLYlink 5.3 years ago
Malachi Griffith
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Hi,

I am in Kenya. I am so much interested in NGS analysis locally. Anybody knows a reputable organization here doing the same. Or alternatively who is ready for partnership to start one good one here.

Beatrice:

ADD REPLYlink 4.1 years ago
betongadi
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Hi,

If you are just starting on NGS, I would strongly recommend you this online course based 100% on R; http://www.biocloudservices.com/NGS-course.html

ADD REPLYlink 3.4 years ago
Bio_ysl
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I like this course about "Analyzing Next-Generation Sequencing Data" from the MSU, I think it's really interesting, specially the focus on AWS EC2. Maybe it can be a bit basic but I think it can be really good to get a general idea about NGS data analysis

Besides, the materials are available under a CC license (http://ged.msu.edu/angus/)

ADD COMMENTlink 8.5 years ago Marina Manrique ♦ 1.3k
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The Canadian bioinformatics workshop has an upcoming workshop on Bioinformatics for Cancer Genomics with a bunch of courses taught by some great investigators from OICR, the University of Toronto, and BCCA. They also have a workshop on High Throughput Sequencing

ADD COMMENTlink 8.5 years ago Gww ♦ 2.6k
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They also now offer a course specifically on RNA-seq analysis: Informatics for RNA-sequence Analysis

ADD REPLYlink 5.3 years ago
Malachi Griffith
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Here is the announcement for the CBW 2015 Workshops: https://www.biostars.org/p/125717/

ADD REPLYlink 5.1 years ago
Malachi Griffith
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Here is another workshop series:

ecSeq Bioinformatics

"ecSeq provides bioinformatics trainings covering the analyses of different high-throughput sequencing experiments. Our customers include large research organisations such as the Max-Planck Institute and the Helmholtz Centre, universities, hospitals, as well as large biotechnology and pharmaceutical companies.

Since 2012 we run public workshops which are continually improved by integrating ideas and suggestions from our participants. This steady feedback loop with our customers helps the workshops stay current with evolving user expectations in NGS data analysis."

ADD COMMENTlink 5.1 years ago Malachi Griffith 17k
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Courses I've heard positive stories about are like at EMBL or the EBI

Also, several of the Wellcome Trust advanced coures have quite a few courses with NGS components or solely on NGS techniques.

But maybe people can better and more specific examples if you tell what kind of courses you're looking for.

ADD COMMENTlink 8.5 years ago Sander Timmer • 700
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Question updated, thanks.

ADD REPLYlink 8.5 years ago
Travis
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The Queensland Brain Institute is running a weekly Seminar Series with focus on the sequencing applications that are used within the Institute (e.g. Genome/Exome-sequencing, RNA sequencing, small RNA sequencing, Methylation analysis,...). All slides are available online and the material for the upcoming discussion groups (hands-on advise for data analysis) will also be made available.

ADD COMMENTlink 8.5 years ago Allpowerde ♦ 1.2k
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It looks good - if only Queensland was closer! Will take a look at the slides, thanks.

ADD REPLYlink 8.5 years ago
Travis
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Seqanswers is an excellent forum with updates/discussions .. its lively and community supported, so all the more impressive!

Here is a post with NGS Blogs: http://seqanswers.com/forums/showthread.php?t=5024

ADD COMMENTlink 8.5 years ago Bioinfosm • 610
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I took the newly created course (given first time this spring) "Genome Bioinformatics" at Uppsala University, to get some grounding for my work at UPPMAX HPC center to support UPPNEX users with NGS analysis. (I had some bioinformatics background, but not specifically in NGS).

The course is heavily focused on NGS analysis, and quickly gave me good insight into the typical NGS analysis workflow, probably much because the course plan revolved around hands-on computer labs, where we got to do all the typical things like alignment, assembly, extract info from fastq files etc [1], while the lectures served to support the hands-on labs with the relevant background theory.

I can highly recommend the course for anyone new to NGS analysis, who is able to spend some four weeks in Uppsala. (Yes, the course is given in English).

[1] Using the typical tools such as samtools, bwa, awk etc, in a linux environment. I also heard from the course organizers that they plan for next year to allow doing the computations at UPPMAX, which will give course participants the added benefit of some HPC experience.

ADD COMMENTlink 8.5 years ago Samuel Lampa ♦ 1.2k
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The Cold Spring Harbor Laboratory hosts several courses relevant to bioinformatics and genomics. The one most related to next generation sequencing analysis is probably: Advanced Sequencing Technologies and Applications. This two week course provides a comprehensive introduction to both laboratory and bioinformatics concepts. Each section combines both theoretical and practical components. The students leave with considerable materials that may prove practical in their own research. The content and style is adjusted each year based on the background and research interests of students accepted into the workshop.

ADD COMMENTlink 7.9 years ago Malachi Griffith 17k
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These NGS events might be of interest: http://www.nature.com/natureevents/science/events/25839-Hands_On_Training_NGS_Data_Analysis

ADD COMMENTlink 5.8 years ago JohnBlue81 • 290
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There is also a recent announcement of workshop in march 2015: https://www.biostars.org/p/120931

ADD COMMENTlink 5.1 years ago Lars • 650
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A Hitchhiker’s Guide to Next Generation Sequencing

This is more of an introduction. But I found it quite useful.

ADD COMMENTlink 8.5 years ago Yogesh Pandit • 500
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ADD COMMENTlink 8.5 years ago Casey Bergman 18k • updated 7.9 years ago Istvan Albert 80k
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Another couple options for series of training workshops:

Data Carpentry

Software Carpentry

ADD COMMENTlink 5.3 years ago Malachi Griffith 17k
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Here is another one:

RNA-Seq Workshop 2015 Announcement


Workshop locations: Dates:
Bowie State University, Bowie, MD June 8-12, 2015
California State University, Long Beach, CA June 22-26, 2015

"We are pleased to update you on Cold Spring Harbor Laboratory DNA Learning Center's (DNALC) National Science Foundation-funded project, _Infrastructure and Training to Bring Next-generation Sequence (NGS) Analysis Into Undergraduate Education._ The goal of this project is to prepare faculty to guide students as co-investigators in novel genome research, focusing on high-throughput RNA-Seq as a tractable entry to NGS. Several faculty participated in our Working Group Retreat held at CSHL in June 2014 and helped refine the RNA-Seq workflow. The Green Line of _DNA Subway, _ an intuitive browser-based interface, supports RNA-Seq analysis and provides an easy biological "on ramp" to the national supercomputing highway. The NSF Proposal Summary and Narrative provides details about the project rationale and structure.

We invite you to apply to attend a 5-day RNA-Seq Workshop in June, 2015. Twenty participants will be selected for each workshop on the basis of their proposal to use and teach RNA-Seq for transcriptome sequencing and genome annotation or differential gene expression. Workshop applications require a formatted RNA-Seq Proposal (Project Proposal Guidelines), a description of course and/or research contexts in which students will be involved, and potential numbers of students involved and duration of exposures (Applicant Information Form [PDF or Word]). A support letter from the department head must be submitted along with the application that demonstrates an institutional commitment to incorporate NGS analysis in appropriate courses and to analyze RNA-Seq datasets during the 2015-16 academic year.

An exciting aspect of this project is available funding to support some faculty at each workshop to develop new RNA-Seq datasets as part of their research. Please keep in mind that the proposed organism must be eukaryotic and have a fully sequenced and annotated genome. These participants must be able to submit high-quality RNA for sequencing by March 3, 2015. The other participants in each workshop will join a funded project or work with an existing dataset. Prior to the workshop, participants can become familiar with the project by visiting the pages of this RNA-Seq website and through participation in project videoconferences."

ADD COMMENTlink 5.1 years ago Malachi Griffith 17k
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There is a course in Raleigh, NC this summer as well!

https://biodatatraining.wordpress.com/

ADD COMMENTlink 5.0 years ago ianmisner17 • 20
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AVLi offers online courses and online trainings. .

ADD COMMENTlink 4.2 years ago aliasgar.babat • 0
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If you are just starting on NGS, I would strongly recommend you this online course; http://www.biocloudservices.com/NGS-course.html

ADD COMMENTlink 3.4 years ago Bio_ysl • 20
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Physalia-courses offers scientific courses and workshops on genomics, transcriptomics, bioinformatics, ecological data and GIS analysis, promoting the transfer of new methods and emerging techniques to a broad range of researchers. Our goal is to build a knowledge-sharing platform between highly qualified instructors and participants at various stage of their scientific and academic career (e.g. PhD students, post-doctoral researchers, PIs). https://www.physalia-courses.org/courses/

ADD COMMENTlink 2.9 years ago carlopecoraro2 • 920

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