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. |