Nanocourse: Compact Data Structures

Start: Sep 2, 2019 01:00 PM (Local Time Germany)
End: Sep 3, 2019 02:30 PM
Speaker: Knut Reinert
Location: MPI-MG
Room: Seminar room 4
Host: Kirsten Kelleher

Second nanocourse of the new IMPRS-BAC. Lectures followed by the opportunity to gain hands-on experience.

Please register for this course by emailing kelleher@molgen.mpg.de

Compact Data Structures have become essential in bioinformatics to deal with large scale genomics data.

For example aligning reads to genomes is usually based on compact representations of efficient full-text indices that are based on the Burrows-Wheeler-Transform, bitvectors and efficient rank and select data structures.
In this course we
* introduce the participants to basic concepts and problems in the field
* exemplify how to think about representing your data compactly
* give some small hands-on examples of the usual time/space tradeoffs when working with implementations (on the second day)

Prerequisites: No fear of computers. Basic C/C++ knowledge. Basic algorithm knowledge.

We will most likely use the SDSL library (https://github.com/simongog/sdsl-lite)
A good source of reading (which is online available for free) is: Gonzalo Navarro, Compact Data Structures (https://www.cambridge.org/core/books/compact-data-structures/68A5983E6F1176181291E235D0B7EB44)