refpkg

Reference package specification

v1.0 Draft

Motivation

To standardize the construction of reference sets for pplacer and other similar tools.

Structure

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.

files

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).

metadata

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

md5 checksums for each of the files to ensure integrity.