mkprobes
mkprobes designs SOLAR probesets — the lab's splint/padlock,
STARmap-style combinatorial FISH assay — from a species' transcriptome. It
covers the full workflow: reference/dataset preparation (including genome +
annotation ingestion for non-traditional model species), target selection,
per-gene candidate generation and off-target screening, probe construction
against a codebook, panel QC, and final assembly into an orderable oligo
pool.
The workflow at a glance:
0. project mkprobes init scaffold a project
1. dataset mkprobes prepare | ingest reference (mouse/human) | any species
2. targets mkprobes chkgenes / convert-to-transcripts
3. codebook mkprobes make-codebook
4. probes mkprobes run-panel candidates -> screen -> construct, all targets in parallel
5. panel QC mkprobes filter-genes
6. assembly mkprobes assemble -> orderable oligos
Where to start
Designing a panel? Getting started is the walkthrough — the whole workflow, start to finish. Everything else is a companion to it.
New to the assay? Read What SOLAR is and what these probes do first: what these probes physically are and why panels are encoded combinatorially.
Setting up a machine? Before you start covers the external programs, the reference files to download, and how much disk, memory and time each step needs.
Not mouse or human? Work through Getting started with SOLAR probesets for a new species open alongside it — that page covers only what differs.
Looking up a flag? CLI reference is generated from the code, so it is always current.
Start here
How-to, step by step