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refpkg
bhodges edited this page Apr 24, 2011
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To standardize the construction of reference sets for pplacer and other similar tools.
A reference package is just a directory with a .refpkg suffix. There will be a CONTENTS.json file describing the files in JSON format. There are three sections: files, metadata, and md5.
Every specified field must appear, but any may be undefined.
Here we describe the sections in order.
- profile
- The alignment profile for the reference alignment.
- taxonomy
- The taxonomic map made by taxtastic.
- aln_fasta
- The reference alignment in fasta format.
- tree_file
- The reference tree in Newick format.
- seq_info
- Mapping from sequence name in tree to taxon id.
- aln_sto
- The reference alignment in Stockholm format.
- phylo_model_file
- A file describing statistics about the phylogenetic model, in JSON format (generated by taxtastic if a supported tree_stats files is specified).
- locus
- The locus described by the reference package (required).
- description
- An arbitrary description field (optional).
- author
- Person who created the reference package (optional).
- create_date
- The date of creation (generated by taxtastic).
- format_version
- Version of the package structure (generated by taxtastic).
- package_version
- The reference package release version (optional).
md5 checksums for each of the files to ensure integrity.