The D. grimshawi dot chromosome
This PowerPoint presentation explains our strategy, detailing the source of the raw sequence data for the D. grimshawi dot chromosome.
Home » Sequence Improvement »
Sequence Improvement
Workflow to Resolve Misassembly
A flowchart that illustrates the key decisions and strategies when dealing with misassemblies that are caused by collapsed repeats.
Common Misassembly Protocols
This document describes a list of protocols that are frequently used to resolve misassembly.
GEP Misassembly Tools User Guide
This document describes the list of tools developed by the GEP to facilitate incorporation of additional reads from the NCBI Trace Archive into a sequence improvement project. This document shows how to install the tools, and illustrates their use in two case studies (walkthroughs) of challenging fosmid assemblies.
Identifying and Sorting Tandem Duplications and an Inverted Repeat
Developed by the professional finishers at the WU Genome Institute (Holly Kotkiewicz and Jennifer Hodges), this walkthrough illustrates how you can use high quality discrepancies, Miniassembly, and cross_match to resolve a major misassembly in a D. ananassae project.
The Finishing Report
This document describes the final student written and oral reports required as part of the Bio 4342 course as taught at WU. In these reports, students describe their work on their fosmid, the challenges they encounter, and the solutions they developed to resolve these challenges.
Finishing Checklist
Students should complete all items on this checklist before submitting the project back to the GEP.
Strategies for Finishing Hybrid Assemblies
This document contains advice on the strategies students can use to resolve common problems they may encounter during sequence improvement.
Calling Additional Reads
Students will typically need to request additional sequencing reactions in order to improve the quality of an assembly. This document describes some of the key considerations that students should keep in mind when they design oligonucleotide primers.
PCR Primer Selection Guide
This document contains advice on the factors that students should consider when designing PCR primers to resolve gaps and low quality regions. The document also includes the specific search parameters students should use to minimize the chance of off-target priming when designing PCR primers.
- « Previous
- 1
- 2
- 3
- Next »