Seal Components

• Bcl2Qseq – BCL to Qseq converter
  • Usage
  • Configurable Properties
• Demux – QSeq demultiplexer
  • Features
  • Usage
  • Output
  • Background
  • Mismatches
  • Sample Sheet
  • Counters
  • Configurable Properties
• PairReadsQSeq
  • Usage
  • Input format
  • Configurable Properties
  • Read Filtering
  • Counters
• Seqal
  • Usage
  • Criteria for duplicate reads
• Seqal Properties
  • Deprecated Properties
• Seqal Counters
• ReadSort
  • Usage
  • Configurable Properties
• MergeAlignments
  • MergeAlignments is not a MapReduce program!
  • Usage
  • Options
  • Examples
• RecabTable
  • Usage
  • Configurable Properties
  • Counters
  • What RecabTable does
  • Output
  • Differences from GATK CountCovariates
  • Limitations
• TsvSort
  • Usage
  • Configurable Properties
  • Weaknesses
• Seal Utilities
  • seal distcp_files
  • seal tsvsort
  • examples/align_script
  • examples/find_fq_format
  • examples/prq_local
  • examples/prq_to_fastq
  • examples/realign_snp