Answers to your question can vary depending on what you want to analyze.
If you are looking for open source platforms where you can directly perform end-to-end WES data analysis, then you can explore platforms such as SanGeniX and Galaxy. In both you can execute WES pipelines easily using the steps stated below. In Galaxy you can create pipeline by connecting each workflow step. In SanGeniX, you can use inbuilt WES analysis pipeline and run multiple samples in batch mode.
In any case, the steps usually involved are
- Checking of quality of sequence reads (FastQC, NGSQC)
- Mapping of reads against reference genome (Bowtie, BWA. Also explore https://omictools.com/read-alignment-category)
- Obtain mapping statistics (samtools, picard)
- Identification of snp (samtools, bcftools, GATK. Explore https://omictools.com/somatic-snp-detection-category)
- Annotation of identified variants (SnpEFF)
- Detection of indels (pindels and others Explore https://omictools.com/indel-detection-category)
- Copy number annotation (Explore https://omictools.com/cnv-annotation-category)
- Structural variant (Explore https://omictools.com/structural-variant-detection-category)
Here is the post you can look at What Is The Best Pipeline For Human Whole Exome Sequencing?
If you want to specifically use Bowtie,here is the tutorial : http://www.cureffi.org/2012/09/07/an-alternative-exome-sequencing-pipeline-using-bowtie2-and-samtools/
The pipeline you will use largely depends on what you want to extract from the exomeseq. Do you want to genotype your samples, do you want to identify mutations or even copy numbers and structural variants? If you further explain what you want to achieve it will be easy for everyone here to provide a more detailed answer.