DocumentCode :
659189
Title :
MCUIUC — A new framework for metagenomic read compression
Author :
Ligo, Jonathan G. ; MinJi Kim ; Emad, Amin ; Milenkovic, Olgica ; Veeravalli, Venugopal V.
Author_Institution :
Dept. of Electr. & Comput. Eng., Univ. of Illinois, Urbana, IL, USA
fYear :
2013
fDate :
9-13 Sept. 2013
Firstpage :
1
Lastpage :
5
Abstract :
Metagenomics is an emerging field of molecular biology concerned with analyzing the genomes of environmental samples comprising many different diverse organisms. Given the nature of metagenomic data, one usually has to sequence the genomic material of all organisms in a batch, leading to a mix of reads coming from different DNA sequences. In deep high-throughput sequencing experiments, the volume of the raw reads is extremely high, frequently exceeding 600 Gb. With an ever increasing demand for storing such reads for future studies, the issue of efficient metagenomic compression becomes of paramount importance. We present the first known approach to metagenome read compression, termed MCUIUC (Metagenomic Compression at UIUC). The gist of the proposed algorithm is to perform classification of reads based on unique organism identifiers, followed by reference-based alignment of reads for individually identified organisms, and metagenomic assembly of unclassified reads. Once assembly and classification are completed, lossless reference based compression is performed via positional encoding. We evaluate the performance of the algorithm on moderate sized synthetic metagenomic samples involving 15 randomly selected organisms and describe future directions for improving the proposed compression method.
Keywords :
DNA; biology computing; data compression; encoding; genomics; molecular biophysics; molecular configurations; DNA sequences; MCUIUC; Metagenomic Compression at UIUC; deep high-throughput sequencing; genomes; individually identified organisms; metagenomic compression; metagenomic read compression; metagenomics; molecular biology; positional encoding; reference-based alignment; unique organism identifiers; Assembly; Bioinformatics; DNA; Genomics; Microorganisms; Sequential analysis;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Information Theory Workshop (ITW), 2013 IEEE
Conference_Location :
Sevilla
Print_ISBN :
978-1-4799-1321-3
Type :
conf
DOI :
10.1109/ITW.2013.6691312
Filename :
6691312
Link To Document :
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