Useful Tools useful-tools

Layout Generators

• Sequencing layout designer
• Sequencing plate layout archive (You need an account to access this page)
  
  
• Guava layout designer
• Guava plate layout archive (You need an account to access this page)

QC and data processing

• Fasta Converter in house fasta-csv conversion tool
• Text to columns Text to Columns tool
• False discovery rate q-value calculator

HIV sequence/function analyses

• HXB2 Genome genome map
• DNA translator DNA translation tool
• Quality Checker Quality Check Tool
• Unique Sequence Finder USF
• Variable Function Analysis in house variable-function analyzer
• Codon by codon in house analysis tool
• Phylogenetic Dating

HLA interpretation and analyses

• HLA class I sequence-based typing interpretation tool
• PHAGE-I-expanded - Proportion of HLA Associated Genomic Escape (individual). PHAGE-I-expanded
  
  

TCR interpretation and analysis

• TCR Distance convert cellranger output for TCR Visualizer
• TCR Visualizer network diagram visualization

Other useful resources

• Primer tables for sequencing or PCR
• Papers about HIV virology, epidemiology, immunology
• Stanford Drug Resistance Database: https://hivdb.stanford.edu/
• LANL HIV Sequence database: https://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html/
• LANL HIV Immunology Database: https://www.hiv.lanl.gov/content/immunology/index.html/