Hack-a-thon session #3 for Test Case #2

28 - 30 August 2013 in Nijmegen, the Netherlands



Test Case #2

First Hack-a-thon in AmsterdamIn August we organise the third hack-a-thon, which is actually the second round of the first hack-a-thon. This hack-a-thon will take place in Nijmegen at CMBI.

The hotel is twenty minutes walking (or a few minutes by car) away.

Hotel Sionshof

Nijmeegsebaan 53 6564 CC Nijmegen the Netherlands +31 (0)24 3227727

We will start Tuesday Aug 27 at 10.15 am.

The meeting ends Thursday Aug 29 at 17:00.

Food will be organised by the hosting institute throughout.

TC Leader: Yael Maoz

Participants:
Yael Maoz
Monika Brandt
Tobias Rausch
Yogesh Paudel
Laurant Falquet
Leon Mei
Wai Yi
Alexander Schoenhuth

Project description

Although many tools designed for structural variation analysis there are no guidelines for bench scientists to help them choose the best tool for their particular data set. In this test case, a researcher is eager to identify large structural variants in multiple accessions of Arabidopsis. What is needed is a tool which can identify the type and quality of the sequencing reads, assemble them with regards to a reference genome, identify SNPs, short indels and large indels, and determine if any annotated genes are associated with the large indels. Lastly, it is desirable that the tool should have a user-friendly interface with which bench scientists can easily examine structural variants in their accession(s) of interest that need to be validated. The long term goal would be to scale up this process to analyse multiple genomes at a time (for example, multiple time points, treatments, or related individuals).

Background from the first hackathon

In the first hackathon, a benchmarking study was performed on synthetic and biological data to test several existing structural variant analysis tools. However, these tools are largely limited to diploid genome analysis and are unable to identify large structural variants (>1Kb) in addition to being unable to identify more complex variants, such as inversions, translocations and copy number variants.

Objective of the second hackathon

Examining larger structural variants and incorporating additional types structural variants, including inversions, translocations and copy number variants into the analysis pipeline we had previously developed. Tools currently available to identify these types of variants include inGAP, SVdetect, CNVnator, CNVseq, DWACseq. We would use simulated data and perform biological testing on a small subset of the tetraploid wheat genome. Following successful testing of the synthetic and validation in a biological setting, we would convert the pipeline into a bench-scientist friendly graphical user interface.

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