Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake

Thompson, Luke R; Anderson, Sean R; Den Uyl, Paul A; Patin, Nastassia V; Lim, Shen Jean; Sanderson, Grant; Goodwin, Kelly D

doi:10.1093/gigascience/giac066

i

Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake

2022
By Thompson, Luke R ; Anderson, Sean R ; Den Uyl, Paul A
Source GigaScience, 2022, 11, 1–12
Series: CIGLR Contribution ; no. 1168

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Journal Title:

GigaScience
Personal Author:

Thompson, Luke R ; Anderson, Sean R ; Den Uyl, Paul A ; Patin, Nastassia V ; Lim, Shen Jean ; Sanderson, Grant ; Goodwin, Kelly D
NOAA Program & Office:

OAR (Oceanic and Atmospheric Research) ; AOML (Atlantic Oceanographic and Meteorological Laboratory) ; CIMAS (Cooperative Institute for Marine and Atmospheric Studies) ; CIGLR (Cooperative Institute for Great Lakes Research)
Description:

Amplicon sequencing (metabarcoding) is a common method to survey diversity of environmental communities whereby a single genetic locus is amplified and sequenced from the DNA of whole or partial organisms, organismal traces (e.g., skin, mucus, feces), or microbes in an environmental sample. Several software packages exist for analyzing amplicon data, among which QIIME 2 has emerged as a popular option because of its broad functionality, plugin architecture, provenance tracking, and interactive visualizations. However, each new analysis requires the user to keep track of input and output file names, parameters, and commands; this lack of automation and standardization is inefficient and creates barriers to meta-analysis and sharing of results.
Keywords:
Source:

GigaScience, 2022, 11, 1–12
Series:

CIGLR Contribution ; no. 1168
DOI:

https://doi.org/10.1093/gigascience/giac066
Document Type:

Journal Article
Funding:

Grant no. NA16OAR4320199 ; Grant no. NA17OAR4320152
Rights Information:

CC BY
Compliance:

Submitted
Download URL:

https://repository.library.noaa.gov/view/noaa/45092/noaa_45092_DS1.pdf
File Type:

[PDF - 3.01 MB]
Collection(s):

Office of Oceanic and Atmospheric Research (OAR) ; NOAA Cooperative Institutes
Main Document Checksum:

urn:sha-512:3e72c5c2527ca08dcd7d58e66f51d5b50949d92d4f80b9fe33f2e4979145b8ca6eb874233758ef0364dfa3814385c2f4744cdb1ce0b86a5178a04c463f81d4b8

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