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

Melissa Gymrek

doi:10.1093/bioinformatics/btu565

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.

Author

Melissa Gymrek¹

Affiliation

¹ Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139 and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139 and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139 and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

PMID: 25147359
DOI: 10.1093/bioinformatics/btu565

Abstract

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 https://mgymrek.github.io/pybamview.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

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