Note: Tick mark means completed tasks. Will be removed in the latter project update documents.
Summary: Finding mutations in HIV RT sequences resistant to drugs from clinical trails and MP samples
- 1. Check automation of Contamination Analysis pipeline on ASPIRE samples
- 2. Work on transferring Contamination Analysis pipeline to NextFlow for packaging
- 3. Work on manuscript on Mutation Analysis & Contamination Analysis
- 4. HIV Mutation Pipeline Update1: Include the code of collecting random virion sequences with condtion of Sample > 25K virions, then randomly select 25K virions.
- 5. HIV Mutation Pipeline Update2: Include the steps for overlap pairs in paired end library. Reference for virion assembly still need to be provided by Kerri to test run this update.
- 6. Work on implementing INT samples with ref6, ref8 and generate mutation report.
Summary: Finding HIV human junctions and assembly of pro-virus
- 1. Conduct test on cutoff position for HIV+Human integration at different percentage coverage vs. length of integration region
- 1. For samples with discrepancy with Kevin's manual assembly, explore reasons and resolve the discrepancy
- 2. For samples which were assembled into provirus sequences, concatenate the assembly of integration region
- 3. Meet with group Friday March 29, 2019 at 12:30 PM
[ ] 1. Work on slides to present the pipelines worked on junction region and provirus assembly
- 1. Continue with the remainder of HIV mutation pipeline
- 2. Discuss if they were able to run and understand each step of the pipeline
- 3. Introduce them with HIV Contamination Analysis pipeline
- 4. Give Traning sesison on complete HIV Contamination Pipeline
- 5. Make Training ppt on Human+HIV integration project
- 6. Make Training ppt on Provirus assembly project