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Paper AssignmentWritten on 11.11.22 by Sven Rahmann Based on your preferences, the papers were assigned. You can find the assignment on the main course page, together with a schedule with important deadlines. Please be especially aware of the HIS/POS registration deadline for the seminar; otherwise you cannot receive graded CP for the… Read more Based on your preferences, the papers were assigned. You can find the assignment on the main course page, together with a schedule with important deadlines. Please be especially aware of the HIS/POS registration deadline for the seminar; otherwise you cannot receive graded CP for the seminar! Please read the paper carefully during the next days. I am continuously available for discussions about the papers during November and December (and also in January for the revisions of the drafts).
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Alignment-free Sequence Analysis Algorithms (Seminar)
In this seminar, we discuss recently published algorithms for alignment free biological sequence analysis, mainly on DNA sequencing data. Starting with an original paper and using the lecture "Algorithms for Sequence Analysis" as background knowledge, participants shall explain a recent method in detail with all necessary additional background.
Both a presentation and a written report are required. An implementation can also be attempted or an existing implementation can be studied on public datasets to check whether the claims made in the paper are true.
A kick-off meeting will be held early in the winter semester. Participation in this kick-off meeting is only possible if you have been assigned to this seminar by the seminar system. You will then receive an email with the exact date and time.
A first draft of the slides and the report are required before the holiday break around Christmas. We will do a peer review, i.e. other students will write a review of your drafts and vice versa. Presentations will be late in the lecture period (the exact dates will be doodled). The final reports are required by the end of the lecture period.
Caution: You cannot register here (in the CMS) directly. You must apply using the seminar system https://seminars.cs.uni-saarland.de. If you are admitted to this seminar, you will be asked to register here. You will also need to register for the seminar exam in LSF separately in due time. Otherwise, you will not get a grade. Please read the "Prüfungsordnung" and "Studienordnung" for all rules and regulations and adhere to them.
Note: A seminar gives 7 CP corresponding to 210 hours of work. This means, you should plan to work approximately 14 h per week every week on average on the seminar material during the lecture period, as there is no work after the lecture period. If you are not ready to invest this amount of time, do not pick this seminar.
Schedule
Thu 03.11. 14:00: Kick-off meeting: presentation of articles (done)
Mon 07.11: 23:59: Choice of papers (done)
Fri 11.11.: Assignment of papers
November and December: office ours to discuss the papers (also via Zoom if necessary), please send email to find a timeslot
Wed 23.11.: Important Deadline for registering the seminar exam in LSF HIS/POS. If you are not registered by the deadline, even if you pass, you will not receive a grade!
31.12.2022: Submission of draft slides and draft summary report to EasyChair for first round of review. I will do a review, and one of the other students.
10.01.2023: Deadline for review submission (via EasyChair)
TBD: day of presentations (slides need to be finished)
10.02.2023: submission of final slides and reports (via EasyChair)
Presentations (Date and Times TBD)
Benjamin: Flexible seed size enables ultra-fast and accurate read alignment
Arthur: Genome assembly with variable order de Bruijn graphs
Simon: KCOSS: an ultra-fast k-mer counter for assembled genome analysis