RT Journal Article
SR Electronic
T1 deSPI: efficient classification of metagenomic reads with lightweight de Bruijn graph-based reference indexing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 080200
DO 10.1101/080200
A1 Dengfeng Guan
A1 Bo Liu
A1 Yadong Wang
YR 2016
UL http://biorxiv.org/content/early/2016/10/12/080200.abstract
AB Summary In metagenomic studies, fast and effective tools are on wide demand to implement taxonomy classification for upto billions of reads. Herein, we propose deSPI, a novel read classification method that classifies reads by recognizing and analyzing the matches between reads and reference with de Bruijn graph-based lightweight reference indexing. deSPI has faster speed with relatively small memory footprint, meanwhile, it can also achieve higher or similar sensitivity and accuracy.Availability the C++ source code of deSPI is available at https://github.com/hitbc/deSPIContact ydwang{at}hit.edu.cnSupplementary information Supplementary data are available at Bioinformatics online.