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
- 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.
- 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
|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.|