Skip to content
/ SMALR Public

SMALR: a framework for single-molecule level interrogation of the methylation status of SMRT reads.

License

Notifications You must be signed in to change notification settings

fanglab/SMALR

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

69 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

SMALR summary

Documentation Status

SMALR: a framework for single-molecule level interrogation of the methylation status of SMRT reads.

The SMALR package conducts single-molecule level interrogation of the methylation status of SMRT reads. There are two protocols available for use within the pipeline, SMsn and SMp.

SMsn: single-molecule, single nucleotide analysis

Each motif site on each sequencing molecule is assessed for methylation status. This is designed for use with short (~250bp) sequencing library preps, where the long read lengths of SMRT reads enables multiple passes over each motif site. The reliability of the SMsn scores increases with more passes (i.e. higher single-molecule coverage).

SMp: single-molecule, motif-pooled analysis

All motif sites on a sequencing molecule are pooled together and the molecule-wide methylation status for the given motif is assessed. This is designed for use with long (10Kb ) sequencing library preps, where each single long subread can span many distinct motif sites. The reliability of the SMp scores increases with increasing number of distinct motif sites contained in the subread.

Documentation

For a comprehensive guide on how to install and run mBin, please see the full documentation.

Citation

Beaulaurier J, Zhang XS, Zhu S, Sebra R, Rosenbluh C, Deikus G, Shen N, Munera D, Waldor MK, A Chess, Blaser MJ, Schadt EE, Fang G. Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. Nature Communications 6, 7438 (2015).

About

SMALR: a framework for single-molecule level interrogation of the methylation status of SMRT reads.

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Languages