Universitá di Pisa –
The human genome is diploid, which requires to assign heterozygous single nucleotide polymorphisms (SNPs) to the two copies of the genome. The resulting haplotypes, lists of SNPs belonging to each copy, are crucial for downstream analyses in population genetics. Currently, statistical approaches, which are oblivious to direct read information, constitute the state-of-the-art. Haplotype assembly, which addresses phasing directly from sequencing reads, suffers from the fact that sequencing reads of the current generation are too short to serve the purposes of genome-wide phasing.
While future-technology sequencing reads will contain sufficient amounts of SNPs per read for phasing, they are also likely to suffer from higher sequencing error rates.
I will describe WhatsHap, the first approach that yields provably optimal solutions to the weighted minimum error correction problem in runtime linear in the number of SNPs. WhatsHap is a fixed parameter tractable (FPT) approach with coverage as the parameter. We demonstrate that WhatsHap can handle datasets of coverage up to 15x, and that 15x are generally enough for reliably phasing long reads, even at significantly elevated sequencing error rates.
I will then show some theoretical results on the optimization problem that lead to HapCol, a fixed parameter algorithm and tool with the number of errors as the parameter. HapCol can handle coverage higher than WhatsHap while being more sensible to the error rate.
Date: 2016-Jun-29 Time: 14:00:00 Room: 408
For more information:
- 21 31 00272
INESC Brussels HUB Winter Meeting | JAN 25-26, 2024, in Porto
The INESC Winter Meeting, organized in collaboration with INESC Holding, is scheduled for January 25th and 26th, 2024, and it will be held in the city of Porto.
On January 25th, the primary goal is to bring together individuals from all five INESC institutes, fostering an environment that encourages networking, forging new connections, and collectively engaging in a forward-thinking exercise regarding the future of our research fields and the positioning of the INESC group within the European landscape.
There will be a welcome lunch, followed by an afternoon dedicated to collaboration, openness, and curiosity. The event will have a participatory approach, and will be guided by Dirk Stockmans, a highly experienced facilitator who has worked for the European Commission for the last 30 years.
Furthermore, all INESC researchers are invited to submit proposals for e-posters to be displayed at the Winter Meeting. Deadline for submissions is December 10 and more information is available here.
On January 26th, a senior administration and management committee will be held. Participants will be selected by each institute administration by invitation only.
If you would to take part on the 25th of January, please register here by November 30th.
The INESC Brussels HUB website will soon share more information about the venue and uptaded agenda.