Pro-/Seminar Bacterial data Summer Term 2015

Bacterial data: Processing and Analysis

This is a block (pro)seminar covering topics related to processing and analysis of NGS data obtained from bacterial genomes: de novo assembly vs. mapping to reference genomes, phylogenetic trees, (alignment-free) variation calling, bacterial resistance studies.

Tutor: Valentina Galata

Dates:

  • Registration: From April 27th to May 1st 2015 (see below for more information)
  • First version of the slides: Deadline May 29th 2015 (4 weeks before the presentation)
  • Presentations: June 26th 2015
  • Summary: Deadline July 3rd 2015 (1 week after the presentation)

Place and Time: E2.1, room 106, 9:00 a.m. s.t.

Registration:

  • From April 27th to May 1st (we will ignore any emails before or after that time period !!!)
  • Plase send the email to the tutor
  • For the registration we need the following information:
    • Your name and matriculation number
    • Bachelor or Master student?
    • In which semester?
    • The topic you prefer (see below)
    • Proseminar or seminar?
    • Do you already have a (pro)seminar certificate
  • Students without any (pro)seminar certificate will be preferred

Requirements for participation:

  • Proseminar: at least in 3rd semester, Bioinformatics I
  • Recommended, but not required: NGS lectures

Requirements for certificate:

  • Submitting the first version of the slides
  • Successful presentation:
    • Talk: 30 minutes (proseminar, in English), 40 minutes (seminar, in English)
    • Questions from the audience (in German or English)
  • Submitting a summary (2 pages, in English)
  • Attendance to all presentations

Topics:

Order Form of presentation Topic Participant
1 Seminar Evaluation and Comparison of Multiple Aligners Shashwat S.
2 Seminar GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers Shounak C.
3 Seminar Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification Saheli D.
4 Seminar Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads Renuka P.
5 Proseminar When Whole-Genome Alignments Just Won’t Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes Sabrina H.
6 Seminar Comparative genomic analysis of Acinetobacter baumannii clinical isolates reveals extensive genomic variation and diverse antibiotic resistance determinants Adnan J.

Some presentation guidelines