Identification of Variants in Bacterial genomes using SNIPPY | Microbial Bioinformatics

This tutorial shows you how to call variants in bacterial genomes using the tool snippy

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Materials
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snippy documentation
github https://github.com/tseemann/snippy

Installation of tools

install anaconda in linux
   • Install , Configure and Run Anaconda ...  
github repo of the yaml file
https://github.com/vappiah/variant-ca...
download link for the yaml file
https://raw.githubusercontent.com/vap...


source of data
https://www.ncbi.nlm.nih.gov/pmc/arti...
sra-database
https://trace.ncbi.nlm.nih.gov/Traces...


Input Files
read 1
http://ftp.sra.ebi.ac.uk/vol1/run/ERR...
read 2
http://ftp.sra.ebi.ac.uk/vol1/run/ERR...
reference genome
https://www.ncbi.nlm.nih.gov/nuccore/...
accession id for reference genome
CP000325.1
contigs
https://raw.githubusercontent.com/vap...
https://raw.githubusercontent.com/vap...


Skip to any section of this tutorial
00:10 intro
02:02 PC requirement
02:35 workflow
03:23 create conda environment and install tools
08:51 activate the conda environment and test the tools
10:11 Download the example data
10:23 sequence reads
15:25 reference genome
21:55 Trim the raw reads
28:50 Variant Calling using fastq files
34:56 Post vcf analysis
58:51 Variant Calling using contigs


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Counting variants
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Genome assembly of illumina reads
   • Genome Assembly Tutorial with SPADes ...  
Download sequences using Python
   • How to  Download sequences from NCBI ...  
Download fastq reads using the sra-toolkit
   • How to DOWNLOAD any Sequence data usi...  




Variant Calling on Bac Snippy | Microbial Bioinformatics | Bioinformatics for Beginners | Course














This section is for the youtube algorithm

samtools
freebayes
bwa
bcftools

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