prophyle 0.1.0.10

ProPhyle metagenomic classifier

Getting started

Prerequisities

• GCC 4.8+

• ZLib

• Python 3 with ete3 library

• SamTools

Recommended way of installation using Conda

Environment installation:

conda create -y --name prophyle \
        -c etetoolkit -c bioconda \
        python==3.4 ete3 bitarray \
        parallel blast samtools=1.3.1

Environment activation:

source activate prophyle

Compile all programs

make -C src

Custom taxonomic trees

Use [bin/build_taxonomic_tree.py](bin/build_taxonomic_tree.py) to build custom taxonomic trees starting from your database’s fasta indexes and taxonomy files ([library/Taxonomy](library/Taxonomy) for more information). Taxonomic identifiers are assigned to the sequences first, and then the tree is built using [ETE Toolkit](http://etetoolkit.org/) and saved as newick format 1. Necessary node attributes are:

• name: unique node name (format n[0-9]*)

• taxid: unique taxonomic identifier

• seqname: names of the sequences sharing the same taxid, separated by @

• fastapath: paths of the sequences’ fasta files, separated by @ (absolute or relative from the main directory of the repository)

• infasta_offset: positions where each sequence starts inside the corresponding fasta files, separated by @

• base_len: length of each sequence, separated by @

Other optional attributes are sci_name, named_lineage, lineage, rank (more info [here](http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html#automatic-tree-annotation-using-ncbi-taxonomy)).