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EMBL-EBI (Cambridge, UK)

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Abstract 2018-2019: Enhancement of pseudochromosome building based on synteny and karyogram staining pattern comparison 

Recent advances in genome sequencing technologies have enabled the generation of complete or partial genome assemblies for a wide variety of species worldwide. Many of these genomes, unlike the assemblies of traditional reference organisms such as Mus musculus and Homo Sapiens, are limited to the contig/scaffold level. The lack of a chromosome level assembly can severely limit the possibility of carrying out a comparative genome analysis between species, e.g. a gene order comparison or a phylogenetic analysis. Because of this limitation, projects such as the Vertebrate Genomes Project (VGP), whose goal it is to create new reference genomes, aim to obtain assemblies on a chromosomal level. At EBI, as part of the VGP, a pipeline has been constructed to build these new reference genomes. While it is nowadays possible to assemble genomes on a chromosomal level, it is important to note that there are only a few computational tools available for this task (e.g. Ragout). Although Ragout has been specifically designed for ordering scaffolds, it is incapable of producing nearly error-free results that are necessary for creating pseudochromosomes. Furthermore, this tool cannot use faulty scaffolds that have been split. To address these limitations, we have developed a software package called SynChroBuild. In the last two months, the code for most functions of the SynChroBuild scripts has been written. The long term goal of this project is to support other types of data input, such as BioNano optical maps, in order to increase the accuracy of the scaffold alignment. Currently, the SynChroBuild package performs a series of necessary steps throughout the entire pseudochromsome building pipeline. It functions as a bridge between the karyogram map and the BLASTN result. The pipeline itself consists of two major sections: one section is the creation of a comparative synteny map, while the other is the construction of the pseudochromosome genome. 

The SynChroBuild package contains two scripts, one for each pipeline section. The first script uses a BLASTN result to create SVG files containing scaffolds that are aligned to their matching reference chromosome(s). By using these files in combination with a corresponding karyogram, the comparative synteny map can be constructed. The second script builds the FASTA file of the pseudochromosomes by using the synteny file as input. This synteny file is derived from the comparative synteny map created in the first section of the pipeline. In addition to its primary functions, SynChroBuild also has several support functions. It is capable of producing AGP files (these files give info about scaffold order and orientation), a BLASTN hit summary file and a synteny summary file. It can also convert SVG files into PDF format. So far the pseudochromosome building of three species has been completed using this new code. While most steps of the pipeline have been made easier with the introduction of SynChroBuild, there is still room for improvement. The code responsible for implementing BioNano optical map data in the scripts still has to be finished. Once completed, this will result in a substantial increase of the accuracy of scaffold ordering. Currently the longest, most labour-intensive step of the pipeline is the construction of the comparative synteny map. The eventual end goal of the SynChroBuild project is to develop a tool capable of integrating inputs from multiple sequencing techniques and from karyotype data in order to construct the pseudochromosome genome by itself.



Saffron Walden CB10
1SD Hinxton
United Kingdom


Traineeship supervisor
Thomas Keane
+ 44 (0) 1223 49 4349
Traineeship supervisor
Jingtao Lilue

Testimony Klaas Vandendriessche (2018-2019)

Hello dear reader. I will start with shortly introducing myself. My name is Klaas Vandendriessche, a bioinformatics student at Howest. I have done my traineeship at EMBL-EBI, a famous international bioinformatics company, located near Cambridge in the United Kingdom. Below you can find some information about my experiences during my traineeship, both in and outside my workplace. First a brief introduction of the United Kingdom and of course the student city of Cambridge. The UK is known for many things. From London’s Big Ben to the Queen, from driving on the left side of the road to using the pound as currency. Even their lack of cooking skills is a typical aspect of the average Brit. However, I will not expand on the capital London, but on the city of Cambridge, located at the river Cam (hence the name). This city is not so far away from London (one hour by train). It is obvious that a lot of students are lodged there. The centre has a lot of parcs and university campuses. The narrow streets, the ancient buildings and museums, the many cosy places and pubs create a nice sphere. As a Belgian you can compare it with Gent. However, Cambridge has still a lot more historical buildings. The EMBL-EBI buildings are located on the Wellcome Genome Campus near Hinxton, a small village in the neighbourhood of Cambridge. The campus is modern with a lot of green areas and parks, where you can take a walk during lunch break. Getting to the company is easy, since the campus organises free buses from and towards Cambridge and its surrounding areas. The total amount of people that work on the campus is around 2600 employees, a mixture of about 70 nationalities. If you come to work here, you will certainly meet colleagues from all over the world. The campus also has several facilities such as restaurants, coffee bars, a gym and a fitness. The average working day for an employee at EMBL-EBI is from 9:00 am until 5:30 pm. My project was writing Python scripts for the creation of pseudochromosomes of rodent species. There is a large amount of study groups at EMBL-EBI that offer a wide variety of tasks, from creating and following genome pipelines to database maintenance and writing scripts. The nine colleagues in my office were all great people with various international backgrounds (Chinese, Indian, Spanish, Finish, Ukrainian, British). 4 Now I am going to give you some information about the financial aspect of my traineeship. To partially sponsor my trip, I received an Erasmus grant. I have travelled to Cambridge by train. I followed the following journey: train Kortrijk – Lille Flanders (10 euros), Eurostar from Lille Europe to London St-Pancras. Direct train from London Kings Cross (located next to St-Pancras station) to Cambridge (17 pounds). The Eurostar tickets (including return) were around 150 euros. However, if you avoid the peak travel hours and book early, you can reduce this amount to around 100 euros. A dayrider ticket (one day unlimited bus travel around Cambridge) costs around 4,50 pounds. I would recommend to avoid a bus subscription, because this is really expensive and not worth paying for, since you most likely will only take the Stagecoach buses during the weekend. My accommodation was located in a landlord’s house in Arbury, a district north of the city centre. I found my accommodation by using the website of the university of Cambridge. If you are going to follow a traineeship at EBML-EBI, the company sends to you a list with all links to websites where you can find all necessary accommodation data. The monthly rent for my room was 456 pounds, about 550 euros per month. Housing in the UK is expensive! However, lodging in Cambridge is much cheaper than, for example, hiring a room in London. Each day I lunched at the campus of EMBL-EBI. The daily costs for lunch are around 4-6 pounds. During the weekends the price highly varied depending on the place where I went to take a meal. My average costs of living, campus lunches not included, were around 15-20 pounds per week. Cambridge offers plenty of opportunities for cultural activities, especially if you are interested in history and science. There are a lot of museums with free entry in and around Cambridge. Here is a list of the ones that I have visited (ranked from the most interesting museum to the less interesting ones): 1) Museum of Archaeology and Anthropology 2) Fitzwilliam Museum 3) Museum of Zoology 4) Museum of Cambridge (not free) 5) Sedgwick Museum of Earth Sciences In the centre of the city there are many pubs and cosy eating places. When it is good weather and if you have some free time, I strongly recommend to take a walk in the botanic gardens of Cambridge. You can find there all kinds of plants, beautiful flowers 5 and sweet-smelling herbs from all over the world. The several beautiful parks in Cambridge are also places where you can stroll and enjoy nature. I have also visited the Duxford airfield to spectate one of their many annual Air Shows. It really was a spectacular event! The costs for my ticket and the snacks that I purchased on the site were in total around 50 pounds. Of course the city of London is also a must to do! You can make a guided vessel tour on the Thames and admire the many beautiful historical buildings such as the Tower Bridge, The British Parliament, the Big Ben clock tower, etc. The price for this one-day trip was around 70 pounds. To conclude, I can say that I definitely enjoyed my stay in Cambridge and working at EMBL-EBI. I would recommend the experience to everyone who is still hesitating to go on an international traineeship. After this traineeship, I felt that I had become much more independent. My view on the world has also broadened a lot by coming in contact with so many different people and cultures. 

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