scholarly journals Succinct Data Structures in the Realm of GIS

2021 ◽  
Vol 7 (1) ◽  
pp. 29
Author(s):  
Nieves R. Brisaboa ◽  
Pablo Gutiérrez-Asorey ◽  
Miguel R. Luaces ◽  
Tirso V. Rodeiro

Geographic Information Systems (GIS) have spread all over our technological environment in the last decade. The inclusion of GPS technologies in everyday portable devices along with the creation of massive shareable geographical data banks has boosted the rise of geoinformatics. Despite the technological maturity of this field, there are still relevant research challenges concerning efficient information storage and representation. One of the most powerful techniques to tackle these issues is designing new Succinct Data Structures (SDS). These structures are defined by three main characteristics: they use a compact representation of the data, they have self-index properties and, as a consequence, they do not need decompression to process the enclosed information. Thus, SDS are not only capable of storing geographical data using as little space as possible, but they can also solve queries efficiently without any previous decompression. This work introduces how SDS can be successfully applied in the GIS context through several novel approaches and practical use cases.

2021 ◽  
Author(s):  
Taher Mun ◽  
Nae-Chyun Chen ◽  
Ben Langmead

AbstractMotivationAs more population genetics datasets and population-specific references become available, the task of translating (“lifting”) read alignments from one reference coordinate system to another is becoming more common. Existing tools generally require a chain file, whereas VCF files are the more common way to represent variation. Existing tools also do not make effective use of threads, creating a post-alignment bottleneck.ResultsLevioSAM is a tool for lifting SAM/BAM alignments from one reference to another using a VCF file containing population variants. LevioSAM uses succinct data structures and scales efficiently to many threads. When run downstream of a read aligner, levioSAM completes in less than 13% the time required by an aligner when both are run with 16 threads.Availabilityhttps://github.com/alshai/[email protected], [email protected]


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