De novo Genome Assembly, 1 hp


Kursnummer60,1
År2017
TypMethodcourse
Spår-
Max antal deltagare25
Sista ansökningsdag2017-09-28
SpråkEn
KursansvarigHenrik Lantz
InstitutionSciLifeLab
BesöksadressUppsala biomedicinska centrum BMC Husarg. 3 751 23 Uppsala
PostadressAdministrativt centrum för SciLifeLab i Uppsala Box 3037 750 03 Uppsala
Datum2017-11-15 to 2017-11-17
LokalE10:1308/1309 (Trippelrummet, Navet)
Kurslängd3 days
Kursrapport 
Kursplan 

 

Beskrivning

National course open for PhD students (prioritized), postdocs, researchers and other employees in need of bioinformatic skills within all Swedish universities.

Inlärningsmål

The course is mostly aimed at researchers getting into their first de novo genome assembly project, but will also include information of use for the more experienced researcher. We will cover assembly of both prokaryotes and eukaryotes (see our sister course in metagenomics for assembly of mixed/environmental samples) and spend a lot of time on learning how to run the analyses in hands-on computer exercises. Applicants will be taken through all steps of a genome assembly project, from the quality assessment of data, through assembly, to validation of assemblies. After this course, the students will be well aware of common practices in genome assembly projects and will know how to avoid common pitfalls.

Innehåll

Topics covered will include:

Different sequencing technologies and their use in genome assembly, including Illumina and PacBio data
Quality assessment of data
Quality based cleaning and adapter trimming
Assembly of genomes including overview of commonly used programs
Assembly validation
Contamination analyses

Undervisning

Applications are only accepted via the course webpage:

https://www.scilifelab.se/events/denovoht17/

Course fee: 1300 SEK.

Entry requirements:
Basic knowledge in linux, some programming/scripting
Desired:Previous experience from working with NGS data

Examination

Participation on all lectures, exercises and discussion.

Litteratur

The literature will be provided during the course.

Lärare

Henrik Lantz

Kontakt

https://www.scilifelab.se/events/denovoht17/

education@scilifelab.uu.se

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