Bioinformatics Training On Next-Generation Sequencing Data

Question

[KS]

Hello Everybody,

I am looking for Bioinformatics Training on Next -Generation sequencing data.

Does anyone know of any short 1 week courses for bioinformatics training on NGS data analysis?

Thanks
Suz

[Bio_ysl]

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

[BioDiscovery]

Hi, you can get all the information here- http://www.biodiscoverygroup.com/JSP/LifeSciences/Workshops.jsp

-Ali.

Answer 1

[Obi Griffith]

If you search the forum for "workshop" you will find quite a lot of previous posts on this topic. This post has lots of information about online bioinformatics training. The two "live training" courses that I am most familiar with are (1) Cold Spring Harbor's Advanced Sequencing Technologies & Applications course which has a whole week of informatics training for NGS analysis and (2) the Canadian Bioinformatics Workshops series which has a session on Informatics of High Throughput Sequencing Data as well as other relevant courses. Both courses are held approximately once per year. The CSH course is very competitive to get into. Other courses which I am not personally familiar with: Duke's Bioinformatics Workshop and the Tri-Institute's (Cornell-MSKCC-Rockefeller) various informatics courses including one on Sequence Analysis.

Wiley has a now slightly dated list of Bioinformatics Training Programs and Courses.

Maybe the best resource is the list of University Bioinformatics Courses that ROSALIND is compiling. They list professors (by country) with personal web-pages that contain links to bioinformatics courses or online materials.

Answer 2

[Nathan S. Watson-Haigh]

Like the other two answers, it's difficult to say without more details. What type of NGS analysis do you want to learn? ChIP-seq, RNA-seq, de novo genome assembly, other? What is your background? Biology, computer science, maths, Bioinformatics?

I'm part of a group running a 2 day, hands-on workshop for biologists in Australia. The workshop contents are released under a creative commons license. See these links for more details:

• http://www.bioplatforms.com.au/workshop2012
• https://github.com/nathanhaigh/ngs_workshop

Cheers, Nathan

[Fidel]

Thanks for releasing the contents under CC!

Answer 3

[A. Domingues]

Without knowing where you are based, how much you are willing to travel and your budget, it is difficult. However, if you are interested in courses in Europe then I suggest looking at those listed in the EMBL site. I recommend the "EMBO Practical Course on Analysis of High-Throughput Sequencing Data". It runs twice a year, teaches the use of free tools (mostly Bioconductor packages but also SAMtools, TopHat, Bowtie). I've attended this year and it was very useful.

Answer 4

[Sukhi Singh]

If you have, the theoretical knowledge about Next generation sequencing, make your mind if you wanna learn remotely or by visiting a workshop. There's almost everything online that you need to learn and try. Read some review paper about technologies and methods, then to have feel for the analyses, start with

Galaxy with screencasts and tutorials, to analyse without less hassle. Once, comfortable with results, then go to the tutorials sections of Biostars, I am sure there's enough there as well, including tiny details/tricks and full explanations and working.

Few posts like workshop-analysis-of-next-generation-sequencing-data, uc-riverside-bioinformatics-manuals, some ppt's like harvard110228DennisWall1.pdf and NGS-workshop-update. will be helpful and will point you to the right direction.

HTH

Cheers

Answer 5

[GAO Yang]

How about the courses held at EMBL-EBI, many of them are about NGS project and data analyse.

For example : Oct 29 2012 - Nov 3 2012 EMBO Practical Course: Analysis of High-Throughput Sequencing Data.

…… Hope helpful :)

Answer 6

[David Langenberger]

Actually, you can do a lot of different bioinformatics analysis for NGS (ChIP-seq, RNA-seq, transcriptome sequencing, miRNA-seq, etc.). If you want to get an overview of all, or get a first/basic idea, of how it might work, these workshops are really nice. Nevertheless, my experience is, that it is always hard to apply the stuff you learn there in your own environment (different machines, different sequencing method/protocol, etc.).

To name one example: I went to one of these RNA-seq courses at EBI. It was great and I really learned a lot. But for the workshop, they used a small example set and mapped/analyzed the data using R. Back in my lab, I tried it and it was not possible for me to use the pipeline at all (my fastq-file was 5GB instead of 2MB and I used the human genome instead of bacteria). So, in the end, it cost me several more weeks to get things done.

What I want to say: These workshops are nice to get a first idea, but every NGS experiment looks completely different and has to be interpreted solely.

---

So, if you have some specific experiment you want to analyze, I recommend one-on-one training sessions. My company offers private trainings. In this training sessions, your data will be used as examples and the complete analysis will run on your machines. We will guide you through the complete process and you have the possibility to ask questions whenever you want. You decide, how the input looks like and how the output should look like. If your sample differs from the regular ones, we will show you how to solve this problem and get the best results out of it. And one of the main advantages is the possibility to choose the tools you want. We recommend you some, but if you want to use, e.g. a specific mapping algorithm, we will help you integrating it into your pipeline.

The main benefit of these one-on-one trainings is the possibility to directly start working after the course. You know, that it works on your machines (everything is already installed), you know how to treat and analyze the data and (based on experience) you will learn much more. In a one-on-one conversation people tend to be not so shy... ending in great discussions and ideas.

Answer 7

[pmlfern]

Hi, I organize a training programme with short hands-on face-to-face courses in Portugal, named GTPB, the Gulbenkian Training programme in Bioinformatics. I think that NGS is needed in almost any thematic course nowadays. My strategy is to insert an NGS module (one day, typically,in each course where it makes sense to see it in action. Examples, you can see the timetables under Detailed Program:

http://gtpb.igc.gulbenkian.pt/bicourses/TA-AFADM12/ had 2 days of RNA-seq;

http://gtpb.igc.gulbenkian.pt/bicourses/GACT12/ had 1 day of NGS use in GWAS, CNV, Linkage Analysis;

http://gtpb.igc.gulbenkian.pt/bicourses/IB12/ had 1 day of NGS Filtering, assembly and mapping;

http://gtpb.igc.gulbenkian.pt/bicourses/RNA12/ had one session on microRNA profiling;

http://gtpb.igc.gulbenkian.pt/bicourses/ANDNMO12/ had lots of NGS (evey day);

http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS12/ was on scripting, automation,workflows for NGS;

http://gtpb.igc.gulbenkian.pt/bicourses/SBTM12/ had onde day of NGS in typing of bacteria;

http://gtpb.igc.gulbenkian.pt/bicourses/HPND12/ had almost 2 days of NGS in the context of ChIP-seq

These are not online courses, the documentation is not really useful a-posteriori for the participants, but parts can be made available on request.

I hope that this helps.

Pedro Fernandes

Answer 8

[Farbod]

Hi

Become a next generation sequencing data scientist

https://www.coursera.org/specializations/genomic-data-science

Answer 9

[pmlfern]

You can also use the BTN website http://www.biotnet.org

Use the Courses and Events TAB engage fillter:courses Text Box:NGS ...... or variants as RNA-seq,etc.

this will only show upcoming courses. remove tha Upcoming events filter that is used by default so that you can also see the past events

Answer 10

[pmlfern]

You can also use the BTN website http://www.biotnet.org

Use the Courses and Events TAB engage fillter:courses Text Box:NGS ...... or variants as RNA-seq,etc.

this will only show upcoming courses. remove tha Upcoming events filter that is used by default so that you can also see the past events

Answer 11

[Bio_ysl]

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

Answer 12

[veb0007]

Auburn University has a one week course once a year http://www.auburn.edu/cosam/bioinformatics/