TURNIP

Introduction

As part of the SGRP project, the NCYC undertook the analysis of the rDNA reads from the resequenced S. cerevisiae and S. paradoxus strains. As a result of this research, the NCYC will be releasing a software suite called TURNIP comprising a set of Perl scripts to aid detection of partial SNPs ('pSNP'), SNPs and indels from unassembled regions of a genome. It is suited to relatively short (10kb - 50kb) regions of DNA, and is able to find sites of microheterogeneity that would otherwise be dismissed through lack of awareness of their existence, or as sequencing error.

Data Visualisation

Results from the analysis of the SGRP dataset are available:
  • Variation Heatmaps and Phylogenetic Trees - Bespoke "heatmap" style visualisations with corresponding phylogenetic trees based on selected variation types.
  • GBrowse - GBrowse implementation showing variation types and frequencies in a classic genome browser interface

Download

The source code for TURNIP is available! Please download the TURNIP source package and read the documentation linked below.

Documentation

TURNIP documentation is available here.

Funding

TURNIP was developed as part of a BBSRC Tools and Resources Development Fund: BB/G000441/1, BB/G00045X/1