ProPhyle metagenomic classifier
Project description
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)).
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