Anglerfish Documentation

Anglerfish is a tool designed to demultiplex Illumina libraries sequenced on Oxford Nanopore flowcells. The primary purpose for this would be to do QC, i.e. to check pool balancing, assess contamination, library insert sizes and so on.

Contents

• Anglerfish
  • Introduction
  • Installation
    • From PyPi
    • From Bioconda
    • Install development version
    • For Arm64 processors (e.g. Apple M2)
  • Source development
  • Usage
    • Options
      • Common
      • --max-unknowns / -u
      • --lenient / -l
      • --ont_barcodes / -n
    • Output files
  • Anglerfish Explore (Experimental)
  • Credits
    • Contributors
• Run demultiplexing, the standard method
  • Use cases
  • Output
  • Mixed setup pools
  • Multiple ONT barcodes
  • Unknown indexes
  • Lenient mode
• Explore demultiplexing, the experimental method
• Troubleshooting