PyBamView: a browser-based application for viewing short read alignments

Bioinformatics. 2014 Dec 1;30(23):3405-7. doi: 10.1093/bioinformatics/btu565. Epub 2014 Aug 21.


Current sequence alignment browsers allow visualization of large and complex next-generation sequencing datasets. However, most of these tools provide inadequate display of insertions and can be cumbersome to use on large datasets. I implemented PyBamView, a lightweight Web application for visualizing short read alignments. It provides an easy-to-use Web interface for viewing alignments across multiple samples, with a focus on accurate visualization of insertions.

Availability and implementation: PyBamView is available as a standard python package. The source code is freely available under the MIT license at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • High-Throughput Nucleotide Sequencing*
  • Internet
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA*
  • Web Browser*