Question: Whole exome sequencing using Bowtie
gravatar for garimav89
3.4 years ago by
garimav890 wrote:

What is the best pipeline for Whole exome sequencing data analysis using Bowtie? Are there any scripts available?

sequencing snp next-gen assembly • 2.4k views
ADD COMMENTlink modified 3.3 years ago by vakul.mohanty240 • written 3.4 years ago by garimav890
gravatar for Persistent LABS
3.4 years ago by
Persistent LABS740 wrote:


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

  1. Checking of quality of sequence reads (FastQC, NGSQC)
  2. Mapping of reads against reference genome (Bowtie, BWA. Also explore
  3. Obtain mapping statistics (samtools, picard)
  4. Identification of snp (samtools, bcftools, GATK. Explore
  5. Annotation of identified variants (SnpEFF)
  6. Detection of indels (pindels and others Explore
  7. Copy number annotation (Explore
  8. Structural variant (Explore



Persistent LABS

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Persistent LABS740


If I want to identify mutations in my cancer samples from exom-seq without having corresponding controls, what would be the pipeline?

ADD REPLYlink written 3.3 years ago by A3.7k
gravatar for Ron
3.4 years ago by
United States
Ron990 wrote:

Hi ,

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 :

ADD COMMENTlink written 3.4 years ago by Ron990
gravatar for vakul.mohanty
3.3 years ago by
United States
vakul.mohanty240 wrote:

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.

ADD COMMENTlink written 3.3 years ago by vakul.mohanty240
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