TY - GEN
T1 - MetaPar
T2 - 2013 1st IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013
AU - Kim, Minji
AU - Ligo, Jonathan G.
AU - Emad, Amin
AU - Farnoud, Farzad
AU - Milenkovic, Olgica
AU - Veeravalli, Venugopal V.
PY - 2013
Y1 - 2013
N2 - We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with low memory usage. The gist of the approach is to iteratively perform read (re)classification based on phylogenetic marker genes and assembler outputs generated from random subsets of metagenomic reads. Once a sufficiently accurate classification within genera is performed, de novo metagenomic assemblers (such as Velvet or IDBA-UD) or reference based assemblers may be used for contig construction. We analyze the performance of MetaPar on synthetic data consisting of 15 randomly chosen species from the NCBI database [18] through the effective gap and effective coverage metrics.
AB - We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with low memory usage. The gist of the approach is to iteratively perform read (re)classification based on phylogenetic marker genes and assembler outputs generated from random subsets of metagenomic reads. Once a sufficiently accurate classification within genera is performed, de novo metagenomic assemblers (such as Velvet or IDBA-UD) or reference based assemblers may be used for contig construction. We analyze the performance of MetaPar on synthetic data consisting of 15 randomly chosen species from the NCBI database [18] through the effective gap and effective coverage metrics.
UR - http://www.scopus.com/inward/record.url?scp=84897710306&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84897710306&partnerID=8YFLogxK
U2 - 10.1109/GlobalSIP.2013.6736807
DO - 10.1109/GlobalSIP.2013.6736807
M3 - Conference contribution
AN - SCOPUS:84897710306
SN - 9781479902484
T3 - 2013 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013 - Proceedings
SP - 43
EP - 46
BT - 2013 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013 - Proceedings
Y2 - 3 December 2013 through 5 December 2013
ER -