Kindly suggest me regarding the protocol and tools for mining of the SNPs by using fastq files.
Thanks
Use fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to check quality of your .fastq files.
If quality is not good enough then go for (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), to process your reads.
Processing include adaptor trimming, poor quality base trimming, length correction etc.
Use Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to align your processed .fastq files with relevant reference genome.
Further information for SNP calling is on (http://bowtie-bio.sourceforge.net/tutorial.shtml).
You can use "https://usegalaxy.org/" to analyse your sequencing data, it have all the tools you needed.
Use fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to check quality of your .fastq files.
If quality is not good enough then go for (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), to process your reads.
Processing include adaptor trimming, poor quality base trimming, length correction etc.
Use Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to align your processed .fastq files with relevant reference genome.
Further information for SNP calling is on (http://bowtie-bio.sourceforge.net/tutorial.shtml).
You can use "https://usegalaxy.org/" to analyse your sequencing data, it have all the tools you needed.
I think you can check NGSEP tool
http://ngsep.sourceforge.net/release213/UserManualNGSEP.pdf
You should probably have a look at the excellent Genome Analysis ToolKit. They provide amazing tutorials, from data pre-processing, to variant calling and mining.
https://software.broadinstitute.org/gatk/
GATK is popular and works well, but it's not always the best:
http://bcb.io/2015/09/17/hg38-validation/
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