TY - JOUR
T1 - Computational Methods for Human Microbiome Analysis
AU - Miossec, Matthieu J.
AU - Valenzuela, Sandro L.
AU - Mendez, Katterinne N.
AU - Castro-Nallar, Eduardo
N1 - Funding Information:
We would like to thank George Washington University's high‐performance computing facility, Colonial One, for providing data storage, support, and computing power for analyses ( http://colonialone.gwu.edu/ ). ECN was funded by FONDECYT de Iniciación and PAI grants number 11160905 and 82140008, respectively.
PY - 2017/11/9
Y1 - 2017/11/9
N2 - As the field of microbiomics advances, the burden of computational work that scientists need to perform in order to extract biological insight has grown accordingly. Likewise, while human microbiome analyses are increasingly shifting toward a greater integration of various high-throughput data types, a core number of methods form the basis of nearly every study. In this unit, we present step-by-step protocols for five core stages of human microbiome research. The protocols presented in this unit provide a base case for human microbiome analysis, complete with sufficient detail for researchers to tailor certain aspects of the protocols to the specificities of their data.
AB - As the field of microbiomics advances, the burden of computational work that scientists need to perform in order to extract biological insight has grown accordingly. Likewise, while human microbiome analyses are increasingly shifting toward a greater integration of various high-throughput data types, a core number of methods form the basis of nearly every study. In this unit, we present step-by-step protocols for five core stages of human microbiome research. The protocols presented in this unit provide a base case for human microbiome analysis, complete with sufficient detail for researchers to tailor certain aspects of the protocols to the specificities of their data.
KW - alpha and beta diversity
KW - differential abundance testing
KW - human microbiome
KW - metagenome decontamination
KW - metagenome reads
KW - read mapping
UR - http://www.scopus.com/inward/record.url?scp=85049260239&partnerID=8YFLogxK
U2 - 10.1002/cpmc.41
DO - 10.1002/cpmc.41
M3 - Article
C2 - 29120486
AN - SCOPUS:85049260239
SN - 1934-8525
VL - 47
SP - 1E.14.1-1E.14.17
JO - Current Protocols in Microbiology
JF - Current Protocols in Microbiology
IS - 1
ER -