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 the best. 

Thanks to all of you for your kind suggestions

GATK is popular and works well, but it's not always the best:

http://bcb.io/2015/09/17/hg38-validation/