CLI Reference¶

designProbes¶

Design probes for the first record in a FASTA file.

designProbes targets.fa --species mouse --channel B1 --output probes.tsv --idt probes.idt

Common flags: - --no-genomemask: skip Bowtie2 uniqueness checks - --index /path/to/index: override Bowtie2 index prefix - --tileSize 52: tile size (probe length before splitting) - --minGC, --maxGC: GC content bounds - --maxProbes: maximum number of probes to emit - --calcPrice: estimate oligo synthesis cost

Note: genome masking is enabled by default and requires a registered species. Use fetchMouseIndex or buildGenomeIndex first, or pass --index to point directly to a Bowtie2 index.

designProbesBatch¶

Design probes for every record in a FASTA file.

designProbesBatch targets.fa --species mouse --channel B1 --output probes.tsv --idt probes.idt

fetchMouseIndex¶

Download a prebuilt mm10 Bowtie2 index and register it under the package indices directory.

fetchMouseIndex

buildGenomeIndex¶

Build a Bowtie2 index for a new reference genome and register it in HCRconfig.yaml.

buildGenomeIndex --species zebrafish --fasta /path/to/genome.fa --threads 8