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

listReferences¶

List all installed reference genomes and their configuration details, including default parameters and the CLI flags needed to use them.

listReferences

Use --config to inspect an alternate configuration file:

listReferences --config /path/to/HCRconfig.yaml

The output shows, for each registered species: - Species name and installation status - Bowtie2 index prefix path (relative and absolute) - Number of index files found on disk - The --species flag to pass to designProbes

It also displays all default parameters from HCRconfig.yaml with their corresponding CLI flags.

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

For large genomes (> 4 billion bases), use the --large-index flag:

buildGenomeIndex --species eberryi --fasta /path/to/genome.fa --threads 8 --large-index