About Course
In Spring 2011, thousands of people in Germany were hospitalized with a deadly disease that started as food poisoning with bloody diarrhea and often led to kidney failure. It was the beginning of the deadliest outbreak in recent history, caused by a mysterious bacterial strain that we will refer to as E. coli X. Soon, German officials linked the outbreak to a restaurant in Lübeck, where nearly 20% of the patrons had developed bloody diarrhea in a single week. At this point, biologists knew that they were facing a previously unknown pathogen and that traditional methods would not suffice – computational biologists would be needed to assemble and analyze the genome of the newly emerged pathogen.

To investigate the evolutionary origin and pathogenic potential of the outbreak strain, researchers started a crowdsourced research program. They released bacterial DNA sequencing data from one of a patient, which elicited a burst of analyses carried out by computational biologists on four continents. They even used GitHub for the project: https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki

The 2011 German outbreak represented an early example of epidemiologists collaborating with computational biologists to stop an outbreak. In this Genome Assembly Programming Challenge, you will follow in the footsteps of the bioinformaticians investigating the outbreak by developing a program to assemble the genome of the E. coli X from millions of overlapping substrings of the E.coli X genome.

------- TIME STAMP --------

THE 2011 EUROPEAN E. COLI OUTBREAK
0:00:00 2011 European E, coli outbreak
0:07:17 Assembling Phage genome

ASSEMBLING GENOME USING DE BRUIJN GRAPHS
0:11:25 DNA arrays
0:16:39 Assembling genomes from k-mers
0:21:02 De Bruijn graphs
0:24:48 Bridges of Königsberg and universal strings
0:29:13 Euler Theorem

GENOME ASSEMBLY FACES REAL SEQUENCING DATA
0:35:29 Splitting the genome into contigs
0:37:35 From reads to read-pairs
0:41:08 Genome assembly faces real sequencing data

⭐ Important Notes ⭐
⌨️ This course is created in collaboration with University of California

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