Reference Genomes¶

Why add a reference genome¶

HCRProbeDesign can check whether candidate probes map uniquely in a genome using Bowtie2. To enable this for species or assemblies beyond the default mouse index, you need to add a Bowtie2 index and register it in HCRconfig.yaml. This lets you: - Run genome masking for non-mouse species or custom assemblies. - Keep indices organized and reusable across runs. - Avoid turning off uniqueness checks with --no-genomemask.

If you do not need uniqueness checks, you can skip this entirely and use --no-genomemask.

How to add a new reference genome¶

1) Prepare a FASTA¶

Download or generate the reference FASTA for your species or assembly. Gzipped FASTA files are supported.

2) Build and register the Bowtie2 index¶

Use buildGenomeIndex to build the index and register it in HCRconfig.yaml.

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

Notes: - --fasta is repeatable and can point to a directory; all .fa, .fasta, or .fna files (including .gz) will be included. - Indices are written under the package indices/ directory by default. - Use --indices-dir to write indices elsewhere and --config to update a specific config file. - Use --force to overwrite an existing index or config entry.

3) Verify the configuration¶

buildGenomeIndex adds an entry like this to HCRconfig.yaml:

species:
  zebrafish:
    bowtie2_index: indices/zebrafish/zebrafish

You can now run probe design with --species zebrafish. If needed, override the index location per run with --index /path/to/index_prefix.

Prebuilt mouse index¶

For mouse (mm10), you can install a prebuilt index instead of building one:

fetchMouseIndex

This registers the mouse entry in HCRconfig.yaml so designProbes --species mouse works immediately.