SMRT Link and Analysis Tools for PacBioData.
The PacBio RS II is ideal for whole-genome sequencing of small genomes, targeted sequencing, complex population analysis, RNA sequencing of targeted transcripts, and microbial epigenetics. The PacBio RS II features high-performance optics, automated liquid handling, proprietary SMRT Cells and reagents, and intuitive instrument control software.
Single-molecule real-time (SMRT) sequencing, developed by Pacific BioSciences (PacBio), offers an alternative approach to overcome many of these limitations. To be concise, it is referred to as “PacBio sequencing” hereinafter, though “SMRT sequencing” is also used by the community.
The SMRT analysis package is open-source and can be downloaded from the PacBio website free of charge. The SMRT Portal, however, is available only for PacBio customers. This means that many users end up with writing their own input.xml and params.xml files.
PacBio SMRT Analysis Server in Docker. GitHub Gist: instantly share code, notes, and snippets.
Once you have ran a base mod pipeline in either SMRT Portal or SMRT Link (via pbsmrtpipe) you should have output.csv,.gff. and cmp.h5 files that you can do tertiary analysis on using whatever you want. There are also a few tools available from PacBio that run downstream of the initial analysis.
SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus Jun Ma, Yixuan Xiang, Yingyuan Xiong, Zhen Lin, Yanbin Xue, Meiqin Mao, Lingxia Sun, Yujue Zhou, Xi Li, Zhuo Huang.
This document describes the underlying command-line interface to SMRT Pipe, and is for use by bioinformaticians working with secondary analysis results. SMRT Pipe is Pacific Biosciences’ underlying analysis framework for secondary analysis functions. SMRT Pipe is a python-based general-purpose workflow engine.