[ buster ]
[ 原始碼： smalr ]
套件：smalr（1.1+dfsg-2）
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.
其他與 smalr 有關的套件
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- dep: bwa (>= 0.7)
- Burrows-Wheeler Aligner
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- dep: cython
- C-Extensions for Python
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- dep: python
- interactive high-level object-oriented language (Python2 version)
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- dep: python-h5py
- general-purpose Python interface to hdf5 (Python 2)
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- dep: python-numpy
- Numerical Python adds a fast array facility to the Python language
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- dep: python-pbcore
- Python 2 library for processing PacBio data files
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- dep: r-base-core (>= 3.0)
- GNU R core of statistical computation and graphics system
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- dep: r-cran-seqinr
- GNU R biological sequences retrieval and analysis
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- dep: samtools
- processing sequence alignments in SAM, BAM and CRAM formats