Bioinformatics Analysis of methicilin-resistant Bacterial strain using nanopore data

Bacterial Genome Analysis of a Methicillin-Resistant Staphylococcus aureus using Nanopore Data (ONT)

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How to Install conda:    • How I install and configure Anaconda in  a...  
How to Install Mamba :    • Install , Configure  and Run Mamba & Conda...  

Original tutorial:https://training.galaxyproject.org/tr...
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Install Jbrowse(Full Installation):    • JBrowse Installation and Usage for Genome ...  
staramr tutorial:   • STARAMR Linux Install and Usage for Antimi...  


Whole Genome Sequence Analysis | Bacterial Genome Analysis | Bioinformatics for Beginners
A bioinformatics tutorial (step-by-step) on how to analyze bacterial genome sequence data.

Whole Genome Sequence Analysis | Bacterial Genome Analysis of Staphylococcus aureus using Nanopore
Whole Genome Sequence Analysis | Bacterial Genome Analysis | Staphylococcus Aureus

Chapters
00:00 Intro
00:07 Where to get the script and ebook
01:58 Activities to be performed
02:30 PC Requirement
03:27 Installing tools using mamba or micromamba(all but jbrowse)
07:08 Create a working environment and cd into it
07:42 Download example data
09:49 Decompress the file using bzip
11:34 Quality Control
12:38 Quality Assessement of the raw_reads using NanoPlot
18:32 Filtering of Long reads using filtlong
21:08 Quality Assessement of filtered reads using NanoPlot
30:15 Genome Assembly of Long Reads(ONT) using Flye
38:03 Visualize the Genome Assemblies using Bandage
49:15 Quality Control (Evaluation) of Genome Assemblies using QUAST
51:07 QUAST output
01:00:07 Identification of Antimicrobial Resistance Genes using STARAMR
01:07:03 STARAMR Output
01:13:18 Genome Assembly Annotation with PROKKA
01:16:06 Exploring the PROKKA Outputs
01:21:42 How to Filter staramr result
01:26:08 Convert the Filtered STARAMR result Table to a GFF file
01:30:15 Mapping Long Reads(ONT) with Minimap2
01:36:27 Visualize the Result using JBROWSE







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