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PUMA: A tool for processing 16S rRNA taxonomy data for analysis and visualization

https://doi.org/10.1101/482380
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/9780471729259.mc01e05s27openalex-snapshot
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
inferredcites →https://doi.org/10.1016/j.tibtech.2017.06.007openalex-snapshot
Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX
inferredcites →https://doi.org/10.1038/ismej.2017.119openalex-snapshot
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
inferredcites →https://doi.org/10.1038/nbt.2676openalex-snapshot
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
inferredcites →https://doi.org/10.1038/nbt.4113openalex-snapshot
Involving undergraduates in genomics research to narrow the education–research gap
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1038/s41592-018-0046-7openalex-snapshot
Bioconda: sustainable and comprehensive software distribution for the life sciences
inferredcites →https://doi.org/10.1093/bioinformatics/btl529openalex-snapshot
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
inferredcites →https://doi.org/10.1093/bioinformatics/btt352openalex-snapshot
Harnessing virtual machines to simplify next-generation DNA sequencing analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btu494openalex-snapshot
STAMP: statistical analysis of taxonomic and functional profiles
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1101/452532openalex-snapshot
Challenges and recommendations to improve installability and archival stability of omics computational tools
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/microbe.11.69.1openalex-snapshot
Transforming Laboratory Education in the Life Sciences
inferredcites →https://doi.org/10.1186/s13742-016-0133-6openalex-snapshot
Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets
inferredcites →https://doi.org/10.1186/s40168-017-0237-yopenalex-snapshot
Normalization and microbial differential abundance strategies depend upon data characteristics
inferredcites →https://doi.org/10.12688/f1000research.16680.1openalex-snapshot
ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations
inferredcites →https://doi.org/10.1371/journal.pcbi.1003531openalex-snapshot
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
inferredcites →https://doi.org/10.1371/journal.pcbi.1005871openalex-snapshot
Ten simple rules for biologists learning to program
inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
inferredcites →https://doi.org/10.1371/journal.pone.0061217openalex-snapshot
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
inferredcites →https://doi.org/10.1371/journal.pone.0148028openalex-snapshot
Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis
inferredcites →https://doi.org/10.1371/journal.pone.0166104openalex-snapshot
Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes
inferredcites →https://doi.org/10.3389/fgene.2018.00212openalex-snapshot
Microbiome Research Is Becoming the Key to Better Understanding Health and Nutrition
inferredcites →https://doi.org/10.3389/fmicb.2016.00459openalex-snapshot
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
inferredcites →https://doi.org/10.3389/fmicb.2019.02407openalex-snapshot
Rarefaction, Alpha Diversity, and Statistics
inferredcites →https://doi.org/10.7287/peerj.preprints.27295v1openalex-snapshot
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
inferredcites →https://doi.org/10.7287/peerj.preprints.3236v1openalex-snapshot
Best practices for conducting benchmarking in the most comprehensive and reproducible way

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/bib/bbz155openalex-snapshot
Current challenges and best-practice protocols for microbiome analysis
inferred← citeshttps://doi.org/10.1128/jmbe.v21i1.1991openalex-snapshot
Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course
inferred← citeshttps://doi.org/10.1155/2020/5738237openalex-snapshot
Analysis of the Soil Microbiome of a Los Angeles Urban Farm
inferred← citeshttps://doi.org/10.3389/fmicb.2020.584699openalex-snapshot
PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom
inferred← citeshttps://doi.org/10.3389/fmicb.2021.681982openalex-snapshot
Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies
inferred← citeshttps://doi.org/10.3733/ca.2021a0001openalex-snapshot
The CALeDNA program: Citizen scientists and researchers inventory California's biodiversity
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.