Whole Genome Sequence Analysis | Bacterial Genome Analysis | Bioinformatics 101 for Beginners
This tutorial shows you how to analyze whole genome sequence of a bacterial genome.
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Materials
__________
Source of Data: https://www.ncbi.nlm.nih.gov/pmc/arti...
Github repository of pipeline :
github.com/vappiah/bacterial-genomics-tutorial
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Chapters
00:01 Introduction
00:26 Analysis workflow
00:48 Where to find the scripts
01:59 Setting up the analysis pipeline
08:43 Running the commands
download the example data
fastqc quality control
trim fastqreads with sickle
genome assembly with spades
evaluating the genome assembly
reference guided scaffolding of the contigs
genome sequence annotation with prokka
multi locus sequence typing
antimicrobial resistance genes detection with abricate
pangenome analysis with roary
genome comparison with BRIG
47:38 Explaining results for ANI-Dendogram
52:36 Explaining results for Pangenome Analysis
58:01 MLST output
58:37 AMR output
58:59 Genome map
Tools Used
Anaconda for software installation
SPADES for genome assembly
PROKKA for genome annotation
ROARY for pangenome analysis
Abricate for antimicrobial gene detection
BRIG for sequence visualization
Python for data visualization
Pilon assembly polishing
FASTQC for Quality Control
QUAST for evaluating genome assembly
RagTag for reference guided scaffolding
quality control
genome assembly
genome annotation
prokka
roary pangenome analysis
genome visualization
A bioinformatics tutorial on Bacterial Whole Genome Sequence Analysis | Comparative Genomics
Whole Genome Sequence Analysis | Bacterial Genome Analysis | Bioinformatics for Beginners
bacteria
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