Difference between revisions of "PacBio sequencing"
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*[[PBcR: Polishing the assembly|<span style="font-size: medium;">Polishing the assembly</span>]] | *[[PBcR: Polishing the assembly|<span style="font-size: medium;">Polishing the assembly</span>]] | ||
*[[PBcR: Output folder structure|<span style="font-size: medium;">O</span><span style="font-size: medium;">utput folder structure</span>]] | *[[PBcR: Output folder structure|<span style="font-size: medium;">O</span><span style="font-size: medium;">utput folder structure</span>]] | ||
| − | *<font size="3">Links</font> | + | *[[PBcR:_Links|<font size="3">Links</font>]] |
Latest revision as of 14:14, 4 May 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
