PROJECT

Scientific background

Goal project

Advances in second and third generation sequencing and optical mapping have made it possible to generate genome sequences on a chromosomal level. By assembling the sequence fragments, we obtain scaffolds with the size of a chromosome (>50Mbp). This allows for the rapid generation of high quality reference genomes for new species. An important source of scaffolding data is chromosome painting/staining (= identify shared karyotype structure).

Chromosome painting data has been obtained from the pseudo chromosomes for the Onychomys species. Advances in automated image processing techniques have been shown to be effective for biological image digitization and alignment. For this project we use similar algorithms and tools to analyze microscope images of chromosome staining (e.g. Q-Banding) to identify shared genomic segments between a reference genome and new rodent species. A variety of rodent species including Acomys, Onychomys and Mus musculus are used to assess the performance of the algorithms. This new algorithm that I help develop will be used as a method for more rapid genome de novo assembly.

Project blog

1 jul 2019
1 minuten

Final progress report

The last weeks of my traineeship at EMBL-EBI basically consisted of fixing some (often hidden) bugs and making some minor improvements to...

27 mei 2019
1 minuten

Report of week 4 and 5

In the previous two weeks I have mostly focused on finishing the ChrBuild2.py script and on expanding the Synteny.py script. My...

12 mei 2019
1 minuten

Report of week 3

This week I finished writing and debugging my first script. The script is called ChrBuild2 and is a major extension of an existing...

6 mei 2019
2 minuten

My daily life at EMBL-EBI

I also want to write something about my daily life on the Wellcome Trust Genome Campus where EMBL-EBI is located. To do this I will...