NDLI: De novo co-assembly of bacterial genomes from multiple single cells

Content Provider	IEEE Xplore Digital Library
Author	Movahedi, N.S. Forouzmand, E. Chitsaz, H.
Copyright Year	2012
Description	Author affiliation: Department of Computer Science, Wayne State University, Detroit, MI 48202 (Movahedi, N.S.; Forouzmand, E.; Chitsaz, H.)
Abstract	Recent progress in DNA amplification techniques, particularly multiple displacement amplification (MDA), has made it possible to sequence and assemble bacterial genomes from a single cell. However, the quality of single cell genome assembly has not yet reached the quality of normal multiceli genome assembly due to the coverage bias and errors caused by MDA. Using a template of more than one cell for MDA or combining separate MDA products has been shown to improve the result of genome assembly from few single cells, but providing identical single cells, as a necessary step for these approaches, is a challenge. As a solution to this problem, we give an algorithm for de novo co-assembly of bacterial genomes from multiple single cells. Our novel method not only detects the outlier cells in a pool, it also identifies and eliminates their genomic sequences from the final assembly. Our proposed co-assembly algorithm is based on colored de Bruijn graph which has been recently proposed for de novo structural variation detection. Our results show that de novo co-assembly of bacterial genomes from multiple single cells outperforms single cell assembly of each individual one in all standard metrics. Moreover, co-assembly outperforms mixed assembly in which the input datasets are simply concatenated. We implemented our algorithm in a software tool called HyDA which is available from http://compbio.cs.wayne.edu/software/hyda.
Starting Page	1
Ending Page	5
File Size	1117331
Page Count	5
File Format	PDF
ISBN	9781467325592
e-ISBN	9781467325608
e-ISBN	9781467325585
DOI	10.1109/BIBM.2012.6392618
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-10-04
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Microorganisms colored de Bruijn graph Image color analysis Genomics DNA Color sequence assembly single cell genomics Bioinformatics Assembly
Content Type	Text
Resource Type	Article

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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