Difference between revisions of "PacBio sequencing"
From mn/ibv/bioinfwiki
(Created page with "= Disclaimer = = SMRT Analysis = == Introduction == == The input.xml file == == The params.xml protocol file == == Read filtering =...") |
|||
| (20 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | = Disclaimer | + | <span style="font-size:large;">Disclaimer</span> |
| + | 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 | + | <span style="font-size:large;">SMRT Analysis</span> |
| − | == | + | *[[SMRT Analysis: Introduction|<span style="font-size:medium;">Introduction</span>]] |
| + | *<span style="font-size:medium;">[[SMRT Analyis: The input.xml file|The input.xml file]]</span> | ||
| + | *<span style="font-size:medium;">[[SMRT Analysis: The params.xml protocol file|The params.xml protocol file]]</span> | ||
| + | *<span style="font-size:medium;">[[SMRT Analysis: Read filtering|Read filtering]]</span> | ||
| + | *<span style="font-size:medium;">[[SMRT Analysis: Read correction|Read correction]]</span> | ||
| + | *<span style="font-size:medium;">[[SMRT Analysis: Mapping reads to a reference|Mapping reads to a reference]]</span> | ||
| + | *[[SMRT Analysis: Assembly|<span style="font-size:medium;">Assembly</span>]] | ||
| + | *[[SMRT Analysis: Viewing HTML reports on Abel|<span style="font-size: medium;">Viewing SMRT Analysis HTML reports on Abel</span>]] | ||
| − | = | + | <span style="font-size:large;">PBrC</span> |
| − | == | + | *[[PBcR: Introduction|<span style="font-size: medium;">Introduction</span>]] |
| − | + | *<span style="font-size: medium;">[[PBcR: Installation|Installation]]</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: Executing the pipeline|<span style="font-size: medium;">Executing the pipeline</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:_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
