16S rRNA gene sequencing is commonly used for identification, classification and quantitation of microbes within complex biological mixtures such as environmental samples and gut samples. Many studies [1][2] are trying to establish the link between the intestinal microbiota with different neurodevelopment, neurogical disorders etc. In these studies the BioInformatic analysis of the data coming from gut samples plays a very important role. So, in our brainhack project we will work on the publicly available data from one of these article[1]. So, this project is aimed for those who are interested in the BioInformatic analysis of Gut Microbiota and are also interested in the different pipelines and analysis tools like QIIME2[4] , cutadapt[5] , Kraken2[6] etc.
In this project, we propose:
To go through this [1] article to understand their method of analyzing the gut microbiota
To download their 16s sequencing data from NCBI ( submitted by the authors )
To extract and filter the data
For advanced users, We also propose:
To write( Python ) few tools for filtering the sequencing data
To try to create an Anaconda environment or a Singularity image with the 16s analysis pipeline QIIME2[4]
To try to implement some of the methods of analysis with QIIME2 ( as described in the article )
To understand the importance of reproducibility of the results
References :
[1] The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota
Patricia Bermudez-Martin et al.
[2] Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease
Timothy R Sampson et al.
The goal of this project to have a basic idea about how the BioInformatics analysis of
16S rRNA sequences are done and also to familiarize with different freely available tools and pipelines
used for the analysis.
Good first issues
Installation of anaconda and create a conda environment
Anaconda or Singularity 50%
Python 50%
Unix/Linux 25%
Basic knowledge about 16s sequencing 25%
Onboarding documentation
No response
What will participants learn?
They will have the basic idea about how the BioInformatic analysis of 16s metagenomic data are done. They will have a preliminary idea about how to search, download and use the open source sequence data from NCBI. They will also learn about many of the state of art open source software tools and pipelines ( which are used for the analysis of 16s data ).
Data to use
No response
Number of collaborators
2
Credit to collaborators
All of the collaborators or participants will have equal credit ...
Image
Type
other
Development status
0_concept_no_content
Topic
reproducible_scientific_methods, other
Tools
other
Programming language
Python, R, shell_scripting, unix_command_line
Modalities
not_applicable
Git skills
4_not_applicable
Anything else?
This is a BioInformatics project where we will focus on a published article and will work on the data submitted by the authors to a public data repository ( NCBI ) ...
Things to do after the project is submitted and ready to review.
[X] Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
dumaatravaie
commented
2 years ago
Title
16s Metagenomic analysis of Gut Microbiome
Leaders
Dipankar Bachar
Collaborators
No response
Brainhack Global 2022 Event
Brainhack Marseille
Project Description
16S rRNA gene sequencing is commonly used for identification, classification and quantitation of microbes within complex biological mixtures such as environmental samples and gut samples. Many studies [1][2] are trying to establish the link between the intestinal microbiota with different neurodevelopment, neurogical disorders etc. In these studies the BioInformatic analysis of the data coming from gut samples plays a very important role. So, in our brainhack project we will work on the publicly available data from one of these article[1]. So, this project is aimed for those who are interested in the BioInformatic analysis of Gut Microbiota and are also interested in the different pipelines and analysis tools like QIIME2[4] , cutadapt[5] , Kraken2[6] etc.
In this project, we propose: To go through this [1] article to understand their method of analyzing the gut microbiota To download their 16s sequencing data from NCBI ( submitted by the authors ) To extract and filter the data
For advanced users, We also propose: To write( Python ) few tools for filtering the sequencing data To try to create an Anaconda environment or a Singularity image with the 16s analysis pipeline QIIME2[4] To try to implement some of the methods of analysis with QIIME2 ( as described in the article ) To understand the importance of reproducibility of the results
References :
[1] The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota Patricia Bermudez-Martin et al.
[2] Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease Timothy R Sampson et al.
[3] https://lcsciences.com/16s-rrna-gene-sequencing-for-identification-classification-and-quantitation-of-microbes/
[4] Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 Evan Bolye et al.
[5] https://cutadapt.readthedocs.io/en/stable/
[6] https://ccb.jhu.edu/software/kraken2/
Link to project repository/sources
https://github.com/dumaatravaie/BrainHack_Marseille_2022_16s
Goals for Brainhack Global
The goal of this project to have a basic idea about how the BioInformatics analysis of 16S rRNA sequences are done and also to familiarize with different freely available tools and pipelines used for the analysis.
Good first issues
Communication channels
https://mattermost.brainhack.org/brainhack/channels/brainhack_marseille_2022_16s_metagenomic
Skills
Anaconda or Singularity 50% Python 50% Unix/Linux 25% Basic knowledge about 16s sequencing 25%
Onboarding documentation
No response
What will participants learn?
They will have the basic idea about how the BioInformatic analysis of 16s metagenomic data are done. They will have a preliminary idea about how to search, download and use the open source sequence data from NCBI. They will also learn about many of the state of art open source software tools and pipelines ( which are used for the analysis of 16s data ).
Data to use
No response
Number of collaborators
2
Credit to collaborators
All of the collaborators or participants will have equal credit ...
Image
Type
other
Development status
0_concept_no_content
Topic
reproducible_scientific_methods, other
Tools
other
Programming language
Python,
R, shell_scripting, unix_command_lineModalities
not_applicable
Git skills
4_not_applicable
Anything else?
This is a BioInformatics project where we will focus on a published article and will work on the data submitted by the authors to a public data repository ( NCBI ) ...
Things to do after the project is submitted and ready to review.
Hi @brainhackorg/project-monitors my project is ready!