Skip to content

Latest commit

 

History

History
22 lines (16 loc) · 1.42 KB

README.md

File metadata and controls

22 lines (16 loc) · 1.42 KB

Pyphillin

(pronounced pie-fillin)

Functional profiles constructed from 16S amplicon sequence data.

Pyphillin is a Python-clone of the functional profiling approach published by SecondGenome in Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes published in PLOS ONE (2016) and Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences. published in BMC Genomics (2020). While the authors demonstrate the benefits of their method, the company has decided to remove access to the research community. Pyphillin is an open-source, freely available clone of Piphillin.

Getting Started

Installation

Pyphillin will be installable trhough the python package index PyPI. This will download the library, create an executable called pyphillin, as well as download the necessary reference databases.

pip install pyphillin

Running

The current beta version of Pyphillin is command-line based. Updates will be coming.

Note: the current version requires the prior installation of VSEARCH https://github.com/torognes/vsearch for performing sequence alignment. The input files required are:

  • taxonomic abundance table in tsv format, with rows representing samples and columns representing ASVs/OTUs
  • representative sequences for the ASVs/OTUs in the taxonomic abundance table, fasta format