The 2016 Workshop on Genomics summary

I recently had the pleasure to spend two and a half weeks in the beautiful medieval town of Český Krumlov, Czech Republic. The reason was the popular Workshop on Genomics that was running and I was one of the TAs involved in making sure everything ran smoothly.

I thought I’d take the opportunity to summarize some of the key events that took place during the workshop since I’ve gathered that there’s some interest reading about the topics that were discussed. For your convenience, I’ve also linked to the pdf lecture slides of each speaker, so you can take a look at their presentation, and to some of the exercises that we ran.

View over Český Krumlov

View over Český Krumlov and its castle

On the first day of the workshop, Evan Eichler gave a fantastic talk about “Genome Structural Variation”. Evan talked about how the human genome is riddled with recently acquired interspersed structural variations, and that we are just now able to better map and understand their causes and consequences.

Evan Eichler

Evan Eichler

Konrad Paszkiewicz educated the eager workshop audience with a lecture on “History of DNA and modern approaches to sequencing”. In his talk, Konrad goes through the new sequencing techniques and how they work in a very pedagogic fashion, making his lecture highly appreciated every year.

Konrad Paszkiewicz

Konrad Paszkiewicz

Julian Catchen

Genomics under chandeliers. Julian Catchen leads participants into the wonderful world of Unix.

The participants learned a wide range of useful skills, including quality control and assessment of reads, using R and RStudio, how to map reads to a reference genome, assemble genomes de novo, annotate and evaluate the assembly, use command-line blast, identify PCR duplicates, call SNPs, and incorporate long PacBio reads.

Mike Zody lecture

Mike Zody speaking about important considerations before sequencing

Mike Zody gave a lecture in “Experimental Design of Sequencing-Based Studies“, where he talked about important considerations before starting a sequencing experiment. If you are planning to use high-throughput sequencing and are wondering how deep you should sequence, what read length to use, which machine to prefer, and how stringent you need to be in filtering the data, take a look at Mike’s very useful slides.

Rayan Chikhi lecture

Rayan Chikhi

Rayan Chikhi engaged the workshop audience with small exercises during his lecture to help them understand assembly algorithms. He also initiated an assembly competition to make participants learn the importance of software parameters and the difference between various N50 statistics.

Gosia Trynka lecture

Gosia Trynka

On Saturday we had the pleasure of listening to Gosia Trynka talk about underlying genomic variants associated with auto-immune diseases in her lecture “Using epigenetic marks for biological interpretation of complex trait associations”.

Sonya Dyhrman

Sonya Dyhrman

And Sonya Dyhrman explained how her lab makes use of high-throughput sequencing techniques in her talk “From flask to field: tracking the drivers of phytoplankton physiological ecology across marine ecosystems”.

Workshop socializing at the pub

Workshop socializing at the pub

Lots of Czech beer and drinks are vital to keep the participants (and TAs) happy and relaxed after a long day of bioinformatics.

Daniel McDonald

Daniel McDonald explains the goals of the QIIME exercise

Paul McMurdie

Paul McMurdie demonstrating the Phyloseq R package

Paul McMurdie and Daniel McDonald kicked off the second week by bringing everyone into the wonderful world of metagenomics and microbiomes.

Beautiful Cesky Krumlov in snow

Beautiful Cesky Krumlov in snow

Bill Cresko

Bill Cresko

Population genomics, RAD-sequencing and how to genomically enable non-model organisms were covered by Bill Cresko’s lecture “Ecological & evolutionary genomic analyses using RAD-seq”. This was followed by Julian Catchen’s Stacks exercise where participants could choose between three different analyses (denovo, reference, phylogenomics), depending on their interests.

Brian Haas

Brian Haas

Wednesday was transcriptomics day. Brian Haas started off with a fantastic lecture on “De novo RNA-Seq Assembly and Transcriptome Studies using Trinity – with Applications towards Non-model Organism Studies”. He continued the day with exercises where participants would assemble a transcriptome de novo and continue annotating and evaluating it with Transdecoder, GOseq and Trinotate.

Chris Wheat

Chris Wheat

Chris Wheat brought everyone down to earth again with his talk “Lies, damn lies, and genomics“, by highlighting some great examples of erroneous conclusions made by high-end publications due to batch effects and differing analysis methods. Important messages to keep in mind when dealing with the massive data that genomic techniques generate.

Toni Gabaldón

Toni Gabaldón

Finally, Toni Gabaldón and Antonis Rokas wrapped up the last two days of the workshop. Toni gave a wonderful lecture on “Ortholog Detection” followed by Antonis’ engaging talk on “Evolutionary Genomics”.

Workshop participants hard at work

Workshop participants hard at work

Thank you to all the participants and everyone involved, making this workshop one of the best in teaching scientists from all over the world genomic and bioinformatic skills.

Disclaimer: All photos taken by me, using my mobile phone, so please excuse the poor quality resulting from dark light conditions.. If you are interested in learning more about the workshop, I suggest you pay the evomics web site a visit.

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About Elin Videvall

Elin is a PhD candidate in the Molecular Ecology and Evolution Lab, Lund University, Sweden. She studies birds and their microbes by analysing genomes, transcriptomes, and microbiomes. You can find her on Twitter: @ElinVidevall
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