Metagenomics Taxonomic Classification using Kraken 2 in BioBam's OmicsBox

In this comprehensive video, I demonstrate how to analyze metagenomics WGS shotgun sequencing data and perform Taxonomic Classification using Kraken 2 in BioBam's OmicsBox tool. I broadly discuss Targeted Sequencing (16S/18S/ITS) and Shotgun WGS, followed by going over metagenomics pipeline and workflow steps and the research questions that metagenomics analysis help to answer. Furthermore, I'll walk you through a compelling case study, discussing study design intricacies to showcase the practical applications of metagenomics analysis.
The complete analysis is performed on BioBam's OmicsBox platform, witnessing firsthand how it simplifies metagenomics research. I'll demonstrate quality control, pre-processing steps, Taxonomic Classification, and interpreting outputs.
This video is in collaboration with BioBam (www.biobam.com/), a prominent bioinformatics solutions company dedicated to creating easy-to-use software for biological research and aiming to bridge the divide between experimental work, bioinformatics analysis, and practical research.
I hope you find this video helpful! Leave your thoughts in the comment section below!
⚠️ Disclaimer:
The content presented on this CZcams video channel is designed exclusively for educational purposes. It should be noted that the creator of the channel makes every possible effort to ensure the accuracy and credibility of the information shared. However, due to the ever-evolving nature of knowledge and certain subjects, occasional inaccuracies or outdated information might occur. Therefore, viewers are strongly advised to complement the provided content with their personal research and seek guidance from qualified professionals or experts before making any decisions or inferences based on the information presented in the videos. Moreover, the perspectives and opinions expressed in the videos are those of the creator alone. They do not necessarily reflect the viewpoints of any affiliated organization, institution, or entity associated with the creator.
▸ Further Inquiries for OmicsBox:
www.biobam.com/contact-us/
▸ OmicsBox Free Trial:
www.biobam.com/trial/
▸ OmicsBox Manual:
manual.omicsbox.biobam.com/us...
▸ Data used for demonstration:
www.ebi.ac.uk/ena/browser/vie...
▸ Associated Publication:
www.ncbi.nlm.nih.gov/pmc/arti...
▸ Github Link for rename script (rename_files.sh):
github.com/kpatel427/CZcamsT...
Chapters:
0:00 Intro
1:02 Metagenomics approaches
2:46 Overview of metagenomics workflow steps
5:45 Questions metagenomics analysis help to answer?
7:36 Case study and study design
8:43 About BioBam
9:32 Exploring OmicsBox
11:06 Downloading metagenomics data
12:35 Performing QC on raw reads using FastQC
13:55 Assessing FastQC report in OmicsBox
17:38 QC Fail: Per Sequence GC Content
18:30 QC Fail: Per Base Sequence Content
20:00 Trimming reads using Trimmomatic
21:51 Assessing Trimmomatic report in OmicsBox
23:26 Post-trimming QC
25:27 Performing Taxonomic classification using Kraken 2
26:38 Exploring Kraken 2 report
28:33 Krona Charts to visualize taxonomic classification
30:37 Principle Coordinate Analysis
33:01 Stacked bar charts to visualize relative abundances of taxa
36:16 Differential Abundance Analysis of taxa
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To get in touch:
Website: bioinformagician.org/
Github: github.com/kpatel427
Email: [e-mail]
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[@ibrahimadiallo1020]

Thank you

[@aris_budiman]

Thank you for your explanation

[@kailashchandhr7240]

Well done

[@Ice84letters]

I am struggling to understand the pre-processing of rnaseq data...should i do it with python? R? command line? i think command line is it easy? what is the best pipeline? fastq-trimmomatric-star? the download of several files from the webpage directly with the command line, manipulate single vs paired ends... you really make excellent videos i do not know if you could talk about this, it would really help me, thanks a lot for all you teach us

[@Ice84letters]

an example from a geodatase for at least two samples paired-end that would be great!!

[@subbaramireddyremala1358]

Could you please post r tutorial for Factorial mendelian randomization, from selecting genetic instruments to analysis. Thankyou

[@quinattasneemrafique536]

Could you kindly suggest me scientific papers you studied to understand the general workflow of Metagenomic analysis. I would be ever grateful.

[@Bioinformagician]

Sure, here are some papers and articles I found helpful:
1. www.ncbi.nlm.nih.gov/pmc/articles/PMC4059276/
2. microbialinformaticsj.biomedcentral.com/articles/10.1186/2042-5783-2-3
3. bioinformaticsworkbook.org/dataAnalysis/Metagenomics/MetagenomicsP1.html#gsc.tab=0
4. scilicium.com/metagenomics-analysis-pipeline/