A New Binning Method for Metagenomics by One-Dimensional Cellular Automata
Author
Source
International Journal of Genomics
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-6, 6 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-10-18
Country of Publication
Egypt
No. of Pages
6
Main Subjects
Abstract EN
More and more developed and inexpensive next-generation sequencing (NGS) technologies allowus to extract vast sequence data from a sample containing multiple species.
Characterizingthe taxonomic diversity for the planet-size data plays an important role in the metagenomicstudies, while a crucial step for doing the study is the binning process to group sequence readsfrom similar species or taxonomic classes.
The metagenomic binning remains a challenge workbecause of not only the various read noises but also the tremendous data volume.
In this work,we propose an unsupervised binning method for NGS reads based on the one-dimensional cellularautomaton (1D-CA).
Our binning method facilities to reduce the memory usage because 1D-CAcosts only linear space.
Experiments on synthetic dataset exhibit that our method is helpful toidentify species of lower abundance compared to the proposed tool.
American Psychological Association (APA)
Lin, Ying-Chih. 2015. A New Binning Method for Metagenomics by One-Dimensional Cellular Automata. International Journal of Genomics،Vol. 2015, no. 2015, pp.1-6.
https://search.emarefa.net/detail/BIM-1065996
Modern Language Association (MLA)
Lin, Ying-Chih. A New Binning Method for Metagenomics by One-Dimensional Cellular Automata. International Journal of Genomics No. 2015 (2015), pp.1-6.
https://search.emarefa.net/detail/BIM-1065996
American Medical Association (AMA)
Lin, Ying-Chih. A New Binning Method for Metagenomics by One-Dimensional Cellular Automata. International Journal of Genomics. 2015. Vol. 2015, no. 2015, pp.1-6.
https://search.emarefa.net/detail/BIM-1065996
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1065996