Difference between revisions of "PacBio sequencing"
From mn/ibv/bioinfwiki
| Line 22: | Line 22: | ||
*[[PBcR: Input file formats|<span style="font-size: medium;">Input file formats</span>]] | *[[PBcR: Input file formats|<span style="font-size: medium;">Input file formats</span>]] | ||
*[[PBcR: Read correction|<span style="font-size: medium;">Read correction</span>]] | *[[PBcR: Read correction|<span style="font-size: medium;">Read correction</span>]] | ||
| − | *<span style="font-size: medium;">Executing the PBcR pipeline | + | *<span style="font-size: medium;">Executing the PBcR pipeline</span> |
| − | *<span style="font-size: medium;">Polishing the | + | *[[PBcR:_Polishing_the_assembly|<span style="font-size: medium;">Polishing the assembly</span>]] |
*<span style="font-size: medium;">PBcR o</span><span style="font-size: medium;">utput folders and formats</span> | *<span style="font-size: medium;">PBcR o</span><span style="font-size: medium;">utput folders and formats</span> | ||
Revision as of 13:37, 30 April 2015
Disclaimer
The following PacBio sequencing walk-through is the result of a few weeks of playing around with the described bioinformatics tools. I am not an expert user of most of these tools, nor do I have in-depth experience with genome assembly. Furthermore, these pages are intended primarily for users affiliated with the University of Oslo (UoO), and with user accounts on the UoO high-performance computing system Abel. If the described tools are installed modules on Abel, I will not describe installation procedures.
This wiki is certain to be incomplete and may sometimes be incorrect. It represents my understanding at the time of writing, and will be updated when required. Use it at your own risc!
SMRT Analysis
- Introduction
- The input.xml file
- The params.xml protocol file
- Read filtering
- Read correction
- Mapping reads to a reference
- Assembly
- Viewing SMRT Analysis HTML reports on Abel
PBrC
- Introduction
- Installation
- Input file formats
- Read correction
- Executing the PBcR pipeline
- Polishing the assembly
- PBcR output folders and formats
