HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

PloS One
Nicholas D YoungblutDaniel H Buckley

Abstract

Combining high throughput sequencing with stable isotope probing (HTS-SIP) is a powerful method for mapping in situ metabolic processes to thousands of microbial taxa. However, accurately mapping metabolic processes to taxa is complex and challenging. Multiple HTS-SIP data analysis methods have been developed, including high-resolution stable isotope probing (HR-SIP), multi-window high-resolution stable isotope probing (MW-HR-SIP), quantitative stable isotope probing (qSIP), and ΔBD. Currently, there is no publicly available software designed specifically for analyzing HTS-SIP data. To address this shortfall, we have developed the HTSSIP R package, an open-source, cross-platform toolset for conducting HTS-SIP analyses in a straightforward and easily reproducible manner. The HTSSIP package, along with full documentation and examples, is available from CRAN at https://cran.r-project.org/web/packages/HTSSIP/index.html and Github at https://github.com/buckleylab/HTSSIP.

References

Aug 4, 2006·Applied and Environmental Microbiology·Tillmann LuedersMatthias Kaestner
Feb 15, 2007·Environmental Microbiology·Feth El Zahar HaicharOdile Berge
Apr 21, 2007·Nature Protocols·Andrew S WhiteleyMike Manefield
Jun 25, 2008·The Science of the Total Environment·Ondrej UhlíkTomas Macek
Aug 21, 2014·Environmental Microbiology Reports·Nicholas D Youngblut, Daniel H Buckley
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Aug 25, 2015·Applied and Environmental Microbiology·Bruce A HungateLance B Price

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Citations

Jul 8, 2018·Applied and Environmental Microbiology·Ömer K CoskunWilliam D Orsi
Sep 15, 2021·Environmental Microbiology·Asa E ConoverEric A Webb
Nov 21, 2021·Proceedings of the National Academy of Sciences of the United States of America·Samuel E BarnettDaniel H Buckley

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Methods Mentioned

BETA
nucleic acid SIP
PCR
RNA-SIP
nucleic

Software Mentioned

Phyloseq R
R package
doSNOW
qSIP
HTSSIP
coenocliner
HTS
DESeq2
SIP R
doParallel

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