Welcome to VATK’s documentation!

Contents:

• Evaluation of sequence data
  • Counting sequences
  • Checking sequence quality
  • Complexity of the sequencing data
• Trimming
  • Tools
  • How to run
  • Benchmark
  • References
• Pre-assembly duplicate removal
• Reference selection
  • Genotype detection
  • Reference selection
  • De-novo assembly
• Alignment/mapping
  • BWA
  • bowtie2
  • Tanoti
• Post-alignment analysis
  • Detecting chimeras
  • Coverage smoothing
  • Further contamination removal
  • Counting and removing duplicates
  • Realignment around indels
  • Removing reads with indels
  • Remove the duplicate fragments
• Reporting alignment stats
  • Depth of coverage
  • Breadth of coverage
  • Standard error and covariance
  • weeSAM
• Pipelines
  • HCMV pipeline

Indices and tables

• Index
• Module Index
• Search Page