SMALR v1.1

Changes

• Added support for current PacBio BAM format of alignments (legacy *.cmp.h5 still supported)
• Moved documentation to readthedocs
• Improved installation procedure by bundling installation of Python dependencies
• Deprecated the --align option due to limited use-cases and limited support with aligned BAM inputs
• Cleaned up codebase

Citation

John Beaulaurier, Xue-Song Zhang, Shijia Zhu, Robert Sebra, Chaggai Rosenbluh, Gintaras Deikus, Nan Shen, Diana Munera, Matthew K. Waldor, Andrew Chess, Martin J. Blaser, Eric E. Schadt & Gang Fang. Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. Nat. Commun. 6, 7438 (2015).

SMALR v1.0

Initial release of SMALR software for single-molecule detection of DNA methylation in SMRT sequencing.

Legal

This release is licensed under the BSD3 open-source license, described in the README file.

Citation

John Beaulaurier, Xue-Song Zhang, Shijia Zhu, Robert Sebra, Chaggai Rosenbluh, Gintaras Deikus, Nan Shen, Diana Munera, Matthew K. Waldor, Andrew Chess, Martin J. Blaser, Eric E. Schadt & Gang Fang. Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. Nat. Commun. 6, 7438 (2015).