Spaced Seed Data Structures for De Novo Assembly
Joint Authors
Birol, Inanç
Chu, Justin
Mohamadi, Hamid
Jackman, Shaun D.
Raghavan, Karthika
Vandervalk, Benjamin P.
Raymond, Anthony
Warren, René L.
Source
International Journal of Genomics
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-8, 8 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-10-11
Country of Publication
Egypt
No. of Pages
8
Main Subjects
Abstract EN
De novo assembly of the genome of a species is essential in the absence of a reference genome sequence.
Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences.
Despite longer subsequences unlocking longer genomic features for assembly, associated increase in compute resources limits the practicability of DBG over other assembly archetypes already designed for longer reads.
Here, we revisit the DBG paradigm to adapt it to the changing sequencing technology landscape and introduce three data structure designs for spaced seeds in the form of paired subsequences.
These data structures address memory and run time constraints imposed by longer reads.
We observe that when a fixed distance separates seed pairs, it provides increased sequence specificity with increased gap length.
Further, we note that Bloom filters would be suitable to implicitly store spaced seeds and be tolerant to sequencing errors.
Building on this concept, we describe a data structure for tracking the frequencies of observed spaced seeds.
These data structure designs will have applications in genome, transcriptome and metagenome assemblies, and read error correction.
American Psychological Association (APA)
Birol, Inanç& Chu, Justin& Mohamadi, Hamid& Jackman, Shaun D.& Raghavan, Karthika& Vandervalk, Benjamin P.…[et al.]. 2015. Spaced Seed Data Structures for De Novo Assembly. International Journal of Genomics،Vol. 2015, no. 2015, pp.1-8.
https://search.emarefa.net/detail/BIM-1065994
Modern Language Association (MLA)
Birol, Inanç…[et al.]. Spaced Seed Data Structures for De Novo Assembly. International Journal of Genomics No. 2015 (2015), pp.1-8.
https://search.emarefa.net/detail/BIM-1065994
American Medical Association (AMA)
Birol, Inanç& Chu, Justin& Mohamadi, Hamid& Jackman, Shaun D.& Raghavan, Karthika& Vandervalk, Benjamin P.…[et al.]. Spaced Seed Data Structures for De Novo Assembly. International Journal of Genomics. 2015. Vol. 2015, no. 2015, pp.1-8.
https://search.emarefa.net/detail/BIM-1065994
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1065994