HCRProbeDesign

HCRProbeDesign is a command-line and Python package for designing HCR v3.0 split-initiator probe pairs from a target FASTA sequence. It tiles target sequences, filters by GC content, melting temperature, homopolymers, and hairpins, and can optionally enforce genome uniqueness with Bowtie2.

Documentation URL: https://www.gofflab.org/HCRProbeDesign/

Key tools

  • designProbes: primary probe design CLI for single-record FASTA inputs
  • designProbesBatch: batch probe design for multi-record FASTA inputs
  • fetchMouseIndex: download, install, and register the mm10 Bowtie2 index
  • buildGenomeIndex: build and register a new reference genome index

Documentation layout

  • Installation and prerequisites
  • Usage walkthroughs and recommended workflows
  • CLI reference with common flags
  • Configuration details for HCRconfig.yaml
  • API reference generated from inline docstrings