MetaSutra

This is the code to run the app described in the manuscript:

Not Available Yet

The app is hosted on Shinyapps.io here:

Not Available Yet

To run this app locally on your machine, download R or RStudio and run the following commands once to set up the environment:

source("server.R")
source("ui.R")
runApp()

You may now run the shiny app with just one command in R:

shiny::runGitHub("MetaSutra", "Nirmal2310")

Nirmal Singh Mahar¹, Anshul Budhraja², Suman Pakala³, Ishaan Gupta¹*, Seesandra V. Rajagopala³*.

¹Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India-110016

²Department of Medicine, Université de Montréal, Quebec, Canada

³Vanderbilt University Medical Center, Nashville, USA

*Corresponding Author

We would appreciate reports of any issues with the app via the issues option of GitHub or by emailing metasutra.help@gmail.com.

Instructions

Instructions can be found here: https://github.com/Nirmal2310/MetaSutra/blob/main/Tabs/additional_information.md

Licensing

This shiny code is licensed under the GPLv3. Please see the file LICENSE.txt for information.

MetaSutra App
Shiny App for analysis and visualization of Metagenomics Data.
Copyright (C) 2024 Nirmal Singh Mahar

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
and this program.  If not, see <http://www.gnu.org/licenses/>.

You may contact the author of this code, Nirmal Singh Mahar, at <bez207518@iitd.ac.in>

Software adapted for use in the pipeline:

• Fastp https://academic.oup.com/bioinformatics/article/34/17/i884/5093234
• BBSuite https://jgi.doe.gov/data-and-tools/software-tools/bbtools/
• SPAdes https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519/
• metaWRAP https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0541-1
• GTDB-tk v2 https://academic.oup.com/bioinformatics/article/38/23/5315/6758240
• RGI https://academic.oup.com/nar/article/48/D1/D517/5608993
• SAMtools https://academic.oup.com/bioinformatics/article/25/16/2078/204688

DOI

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