Transposon Insertion Sequencing Analyses using Galaxy, BioConda and public research infrastructure (XSEDE, de.NBI-cloud, ARDC cloud)
Delphine Larivière, Anton Nekrutenko
This repository serves as a companion to our study assessing the computational tools for Transposon Insertion Sequencing analyses:
Reproducible and accessible analysis of transposon insertion data at scale Delphine Larivière, Laura Wickham, Kenneth Keiler, Anton Nekrutenko
It contains descriptions of workflows and exact versions of all software used. The goals of this study were to:
- Identify the methods used for TIS analyses in the litterature
- Identify the best ones to use for the two most common types of TIS data
- Implement robust and accessible analyses workflows for these two types of data
Our analysis was divided into two parts listed below. Each part has a dedicated directory containing results of our analyses, and jupyter notebooks describing the manual analyses described in the paper. Galaxy workflows described in the paper can be find here :
The analyses have been performed using the Galaxy platform and open source tools from BioConda. Tool runs used XSEDE resources maintained by the Texas Advanced Computing Center (TACC), Pittsburgh Supercomputing Center (PSC), and Indiana University in the U.S., de.NBI and VSC cloud resources on the European side, and ARDC cloud resources in Australia.
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