TY - JOUR
T1 - TIPP2
T2 - Metagenomic taxonomic profiling using phylogenetic markers
AU - Shah, Nidhi
AU - Molloy, Erin K.
AU - Pop, Mihai
AU - Warnow, Tandy
N1 - Funding Information:
This work was supported by the US National Science Foundation awards 1513629 to T.W. and 1513615 to M.P. This study was performed on the Illinois Campus Cluster and the Blue Waters supercomputer, resources operated and financially supported by UIUC in conjunction with the National Center for Supercomputing Applications. Blue Waters is supported by the NSF [OCI-0725070, ACI-1238993] and the State of Illinois.
Publisher Copyright:
© 2021 The Author(s) 2021. Published by Oxford University Press.
PY - 2021/7/1
Y1 - 2021/7/1
N2 - Motivation: Metagenomics has revolutionized microbiome research by enabling researchers to characterize the composition of complex microbial communities. Taxonomic profiling is one of the critical steps in metagenomic analyses. Marker genes, which are single-copy and universally found across Bacteria and Archaea, can provide accurate estimates of taxon abundances in the sample. Results: We present TIPP2, a marker gene-based abundance profiling method, which combines phylogenetic placement with statistical techniques to control classification precision and recall. TIPP2 includes an updated set of reference packages and several algorithmic improvements over the original TIPP method. We find that TIPP2 provides comparable or better estimates of abundance than other profiling methods (including Bracken, mOTUsv2 and MetaPhlAn2), and strictly dominates other methods when there are under-represented (novel) genomes present in the dataset.
AB - Motivation: Metagenomics has revolutionized microbiome research by enabling researchers to characterize the composition of complex microbial communities. Taxonomic profiling is one of the critical steps in metagenomic analyses. Marker genes, which are single-copy and universally found across Bacteria and Archaea, can provide accurate estimates of taxon abundances in the sample. Results: We present TIPP2, a marker gene-based abundance profiling method, which combines phylogenetic placement with statistical techniques to control classification precision and recall. TIPP2 includes an updated set of reference packages and several algorithmic improvements over the original TIPP method. We find that TIPP2 provides comparable or better estimates of abundance than other profiling methods (including Bracken, mOTUsv2 and MetaPhlAn2), and strictly dominates other methods when there are under-represented (novel) genomes present in the dataset.
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U2 - 10.1093/bioinformatics/btab023
DO - 10.1093/bioinformatics/btab023
M3 - Article
C2 - 33471121
SN - 1367-4803
VL - 37
SP - 1839
EP - 1845
JO - Bioinformatics (Oxford, England)
JF - Bioinformatics (Oxford, England)
IS - 13
ER -