Interactive genome viewer (IGV)

Interactive Genome Viewer is a high performance, powerful visualization tool for large genomic data sets. It supports a wide variety of data types such as

• Next generation sequencing data
• SAM files
• Array based data
• other genomic data sets

IGV is a basic data visualization and exploration tool such as whole exome sequencing data, whole genome sequencing data and much more.IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license. IGV  is a desktop application written in JAVA Programming language and works on many platforms like windows, MAC and LINUX.

A primary design goal of IGV is to support interactive exploration of large-scale genomic data sets on standard desktop computers. It supports multiple file formats for genomic data such as

• BED
• BAM
• SNP files

It allows investigators to  visualize many different types of data together—and importantly also integrate these data with the display of sample attribute information such as clinical and phenotypic information. To support interactive exploration of data, IGV provides direct manipulation navigation in the style of Google Maps. For instance, you click and drag to pan the view across the genome and double-click on a region to zoom in for a more detailed view. It supports real-time interaction at all scales of genome resolution, from whole genome to base pairs, even for very large data sets. The Broad IGV data server hosts many genome annotation files and data sets from a variety of public sources (including from TCGA, 1000 Genomes Project, ENCODE Project  and others). 

Step by step procedure to visualize genomic reads

1) Install IGV on your computers by downloading it from (www.broadinstitute.org/igv)

2) Get familiar with the control pane of IGV windows

IGV windows

3)  Select the reference genome before loading the data. select genome option is given in toolbar at the top of IGV window. IGV provides dozens of hosted reference genomes to choose from, but also provides the option of importing others from the sequence data. The minimal requirement for importing a genome is a FASTA file containing chromosome or contig sequences. 

4) Now load your genomic data

5)After aligning the reads on reference genome of interest visualize the alignment.

7) Visualize the insertions, deletions and SNP,s along with their Allele frequencies and details of amino acid changes.

Alignment on reference genome and visualization of both reverse and forward strands

For any queries regarding its working feel free to comment :)