skip to main content


Title: MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data
Abstract Background

Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking.

Results

Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses.

Conclusion

Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and aSphagnumleachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively.

 
more » « less
NSF-PAR ID:
10397651
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ;
Publisher / Repository:
Springer Science + Business Media
Date Published:
Journal Name:
Microbiome
Volume:
11
Issue:
1
ISSN:
2049-2618
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Background

    Differential correlation networks are increasingly used to delineate changes in interactions among biomolecules. They characterize differences between omics networks under two different conditions, and can be used to delineate mechanisms of disease initiation and progression.

    Results

    We present a new R package, , that facilitates the estimation and visualization of differential correlation networks using multiple correlation measures and inference methods. The software is implemented in , and , and is available athttps://github.com/sqyu/CorDiffViz. Visualization has been tested for the Chrome and Firefox web browsers. A demo is available athttps://diffcornet.github.io/CorDiffViz/demo.html.

    Conclusions

    Our software offers considerable flexibility by allowing the user to interact with the visualization and choose from different estimation methods and visualizations. It also allows the user to easily toggle between correlation networks for samples under one condition and differential correlations between samples under two conditions. Moreover, the software facilitates integrative analysis of cross-correlation networks between two omics data sets.

     
    more » « less
  2. Abstract Background

    The pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species.

    Results

    Here we introduce PGV, a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering. Our experimental results demonstrate that PGV enables an intuitive, effective and interactive visualization of a pan-genome by providing a genome browser that can elucidate complex structural genomic variations.

    Conclusions

    The PGV software can be installed via conda or downloaded fromhttps://github.com/ucrbioinfo/PGV. The companion PGV browser athttp://pgv.cs.ucr.educan be tested using example bed tracks available from the GitHub page.

     
    more » « less
  3. A<sc>bstract</sc>

    We presentνDoBe, a Python tool for the computation of neutrinoless double beta decay (0νββ) rates in terms of lepton-number-violating operators in the Standard Model Effective Field Theory (SMEFT). The tool can be used for automated calculations of 0νββrates, electron spectra and angular correlations for all isotopes of experimental interest, for lepton-number-violating operators up to and including dimension 9. The tool takes care of renormalization-group running to lower energies and provides the matching to the low-energy effective field theory and, at lower scales, to a chiral effective field theory description of 0νββrates. The user can specify different sets of nuclear matrix elements from various many-body methods and hadronic low-energy constants. The tool can be used to quickly generate analytical and numerical expressions for 0νββrates and to generate a large variety of plots. In this work, we provide examples of possible use along with a detailed code documentation. The code can be accessed through:

    GitHub:https://github.com/OScholer/nudobe

    Online User-Interface:https://oscholer-nudobe-streamlit-4foz22.streamlit.app/

     
    more » « less
  4. Abstract Background

    Direct-sequencing technologies, such as Oxford Nanopore’s, are delivering long RNA reads with great efficacy and convenience. These technologies afford an ability to detect post-transcriptional modifications at a single-molecule resolution, promising new insights into the functional roles of RNA. However, realizing this potential requires new tools to analyze and explore this type of data.

    Result

    Here, we present Sequoia, a visual analytics tool that allows users to interactively explore nanopore sequences. Sequoia combines a Python-based backend with a multi-view visualization interface, enabling users to import raw nanopore sequencing data in a Fast5 format, cluster sequences based on electric-current similarities, and drill-down onto signals to identify properties of interest. We demonstrate the application of Sequoia by generating and analyzing ~ 500k reads from direct RNA sequencing data of human HeLa cell line. We focus on comparing signal features from m6A and m5C RNA modifications as the first step towards building automated classifiers. We show how, through iterative visual exploration and tuning of dimensionality reduction parameters, we can separate modified RNA sequences from their unmodified counterparts. We also document new, qualitative signal signatures that characterize these modifications from otherwise normal RNA bases, which we were able to discover from the visualization.

    Conclusions

    Sequoia’s interactive features complement existing computational approaches in nanopore-based RNA workflows. The insights gleaned through visual analysis should help users in developing rationales, hypotheses, and insights into the dynamic nature of RNA. Sequoia is available athttps://github.com/dnonatar/Sequoia.

     
    more » « less
  5. Abstract Background

    Low-depth sequencing allows researchers to increase sample size at the expense of lower accuracy. To incorporate uncertainties while maintaining statistical power, we introduce to analyze population structure of low-depth sequencing data.

    Results

    The method optimizes the choice of nonlinear transformations of dosages to maximize the Ky Fan norm of the covariance matrix. The transformation incorporates the uncertainty in calling between heterozygotes and the common homozygotes for loci having a rare allele and is more linear when both variants are common.

    Conclusions

    We apply to samples from two indigenous Siberian populations and reveal hidden population structure accurately using only a single chromosome. The package is available onhttps://github.com/yiwenstat/MCPCA_PopGen.

     
    more » « less