Pipits

Description

pipits website  

PIPITS is an automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform.

PIPITS is designed to work best on Bio-Linux (http://environmentalomics.org/bio-linux/) and Ubuntu. Unfortunately, it's NOT supported on Windows or a Mac

If you are using Bio-Linux, most of the dependencies are already on Bio-Linux. Otherwise, you will have to set up the dependencies yourself. If you are using Ubuntu, then instructions on how to set up dependencies are described below (1.8).

Required Modules

Serial

• gcc/5.2.0
• pipits

System Variables

• HPC_{{#uppercase:pipits}}_DIR - installation directory

Citation

If you publish research that uses pipits you have to cite it as follows:

Hyun S. Gweon, Anna Oliver, Joanne Taylor, Tim Booth, Melanie Gibbs, Daniel S. Read, Robert I. Griffiths and Karsten Schonrogge, PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform, Methods in Ecology and Evolution, DOI: 10.1111/2041-210X.12399