Phylogenetic Read Placement Protocol v1

This protocol is for phylogenetic read placement of metagenomic reads in as quantitative a manner as possible without addition of known standards. This protocol includes assembly of metagenomes into contigs, creation of phylogenetic trees including proteins from assembled contigs, the phylogenetic read placement of metagenomic reads onto the tree, taxonomic identification, and collation by taxonomy and metagenomic sample. Several published software are used in this protocol, but here we share our scripts for using the outputs from this software in as quantitative a manner as is possible. This protocol is a daughter protocol to the PHAN-C pipeline which is available online, but our protocol using more recently published programs including epa-ng, gappa, and RaxML-ng.