Open NGS Browser to visualize and explore short-read sequence alignments
ngsbrowser opens the NGS Browser app, from which you can import:
A single reference sequence from a FASTA-formatted file
Short-read sequence alignment data from SAM- or BAM-formatted files or BioMap objects
Annotation features from GFF- or GTF-formatted files
You can then visualize and explore the alignments and feature annotations.
This example shows how to create a BioMap object and display in the NGS Browser.
Create a BioMap object from a SAM-formatted file.
b = BioMap('ex1.sam');
Display the object in the NGS Browser.
Use the NGS Browser to compare the alignment of multiple data sets to a common reference sequence.
Use the NGS Browser to investigate regions of interest in the short-read alignment determined by various analyses, such as RNA-Seq, ChIP-Seq, and genetic variation analyses.