Package: smalr (1.1+dfsg-2)

[ Source: smalr  ]

interrogation of the methylation status of nucleotide sequencing reads

The SMALR package conducts single-molecule level interrogation of the methylation status of single-molecule real-time (SMRT) sequencing 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.

Other Packages Related to smalr

• dep: bwa (>= 0.7)

  Burrows-Wheeler Aligner

• dep: cython

  C-Extensions for Python

• dep: python

  interactive high-level object-oriented language (Python2 version)

• dep: python-h5py

  general-purpose Python interface to hdf5 (Python 2)

• dep: python-numpy

  Numerical Python adds a fast array facility to the Python language

• dep: python-pbcore

  Python 2 library for processing PacBio data files

• dep: r-base-core (>= 3.0)

  GNU R core of statistical computation and graphics system

• dep: r-cran-seqinr

  GNU R biological sequences retrieval and analysis

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

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