Parallel efficient alignment of reads for re-sequencing applications
Departamento de Engenharia Informática –
In bioinformatics, in the context of resequencing projects,
the e cient and accurate mapping of reads to a reference
genome is a critical problem. One instance of this problem
is the local alignment of pyrosequencing reads produced
by the 454 GS FLX system against a reference sequence,
an instance for which the software tool TAPyR (Tool for
the Alignment of Pyrosequencing Reads) was developed.
TAPyR implements a methodology to e ciently solve this
problem, which proved to yield results of a quality (both in
terms of content and execution speed) higher than those of
mainstream applications. With the goal of further improving
this platforms results, we produced a parallel implementation
of the query and reference sequence access procedures
of the original version. Through the use of multithreading,
this new version, P-TAPyR, produces considerable
reductions in the processing time of queries, scaling with
the amount of hardware-supported threads (not accounting
for hyper-threading) available. For larger data sets, we
were able to observe running times roughly 26 times faster
than serial execution with 30 executing threads, showing
an experimental (progressively-decreasing) execution serial
fraction of 0.8% (determined by the Karp-Rabin Metric described
in a posterior section). Herein we present the modi
cations made to this software tool to allow for parallel
querying of reads against an indexed reference which, scales
proportionally to the amount of available physical cores.
Date: 2013-Sep-26 Time: 11:00:00 Room: 336
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Workshop “Metabolism and mathematical models: Two for a tango” – 2nd Edition
Title: Workshop Metabolism and mathematical models: Two for a tango – 2nd Edition
Dates: October 25-26, 2022
Location: This workshop will be held in a virtual way
The topic of this workshop is metabolism in general, with a special focus, although not exclusive, on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences – Inria Associated Team Capoeira – and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg – H2020 Twinning Project Olissipo.
The workshop is open to all members of these two projects but also, importantly, to the community in general.
The program and more details are available here.