Pro-/Seminar Efficient Data Structures in Computational Microbiological Research Winter Term 2016/2017

Efficient Data Structures in Computational Microbiological Research

This is a block (pro)seminar covering topics related to efficient data structures in computational microbiological research. It is intended for Bioinformatics students only.

Tutor: Cedric Laczny

Dates:

Registration From October 25th to November 1st, 2016 – HERE
De-registration deadline Februar 1st, 2017
Kick-off meeting January 18th, 2017 – 15:00 s.t – E2.1 room 206
Deadline for the 1st version of slides February 13th, 2017
Presentations March 13th, 2017 – 09:00 s.t – E2.1 room 206
Summary submission deadline March 20th, 2017

Place and Time:

  • E2.1, room 206, 09:00 s.t.

Requirements for participation:

  • Proseminar: at least in 3rd semester, Bioinformatics I

Certificate requirements:

  • Submitting the first version of the slides (see presentation guidelines and presentation guidelines checklist)
  • Successful presentation:
    • Talk: 30 minutes (proseminar); 40 minutes (seminar)
    • Questions from the audience after the presentation
  • Attendance to all presentations
  • Submitting a summary (ca. 2 pages)

Topics: As indicated by the title of this course, the emphasis is on the efficient data structures, rather than any detailed biological results.

Nr. Presentation Topic Participant
1 Seminar Scaling metagenome sequence assembly with probabilistic de Bruijn graphs Andreas D.
2 Seminar Mash: fast genome and metagenome distance estimation using MinHash Vanessa S.
3 Seminar Kraken: ultrafast metagenomic sequence classification using exact alignments Waqas D.
4 Seminar Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences Ngaha J.
5 Seminar MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Khushboo A.