What makes refgenie better?

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1. It provides a command-line interface to download individual resources. Think of it as GitHub for reference genomes. You just type refgenie pull hg38/bwa_index.
2. It’s scripted. In case you need resources not on the server, such as for a custom genome, you can build your own: refgenie build custom_genome/bowtie2_index.
3. It simplifies finding local asset locations. When you need a path to an asset, you can seek it, making your pipelines portable across computing environments: refgenie seek hg38/salmon_index.
4. It provides remote operation mode, useful for cloud applications. Get a path to an asset file hosted on AWS S3: refgenie seekr hg38/fasta --remote-class s3.
5. It includes a Python API. For tool developers, you use rgc = refgenconf.RefGenConf("genomes.yaml") to get a Python object with paths to any genome asset, e.g., rgc.seek("hg38", "kallisto_index").
6. It strictly determines genomes compatibility. Users refer to genomes with arbitrary aliases, like “hg38”, but refgenie uses sequence-derived identifiers to verify genome identity with asset servers.

Commands

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Install and configure

pip install --user refgenie
export PATH=~/.local/bin:$PATH
refgenie init -c data/reference_data/genome_config.yaml
export REFGENIE=data/reference_data/genome_config.yaml
refgenie listr

Download pre-built reference genome assets

The listr command lists remote assets to see what’s available: refgenie listr

The pull downloads the specific asset of your choice: refgenie pull GENOME/ASSET

Where GENOME refers to a genome key (e.g. hg38) and ASSET refers to one or more specific asset keys (e.g. bowtie2_index). For example: refgenie pull hg38/bowtie2_index

You can also pull many assets at once: refgenie pull --genome mm10 bowtie2_index hisat2_index

Refer to assets

refgenie seek rCRSd/fasta path/to/genomes/archive/rCRSd/fasta/default/rCRSd.fa