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.


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Create a BioMap Object and Import it to the NGS Browser

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.


More About

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  • 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.

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