SATAY analysis workflow

Our first release of the pipeline has now a DOI :) to be citable, and findable!!!

Look our documentation using Jupyter Book 🎆🎉

Overview

This workflow is created for processing sequencing data for SAturated Transposon Analysis in Yeast (SATAY) for Saccharomyces Cerevisiae. It performs the steps from raw sequencing data until the transposon mapping that outputs files containing all insertion sites combined with the number of reads. For more information about this project, see our JupyterBook. For more information regarding SATAY, see the satay user website created by the Kornmann-lab.

For a complete guide how to use it, see the documentation.

Features

The workflow requires input sequencing data in fastq format. It can perform the following tasks:

• sequence trimming
• quality checking raw and trimmed fastq files
• sequence alignment with reference genome (S288C Cerevisiae genome)
• quality checking bam files, indexing and sorting
• transposon mapping

The output files indicate the location of transposon insertions and the number of reads at those locations. This is presented in both .bed and .wig format. Also a list of genes is generated where the number and distribution of insertions and reads is presented per (essential) gene.

Running the project

The main workflow is called satay.sh and runs in Linux. Start the workflow using the command bash satay.sh. NOTE: Before starting the workflow on your Linux machine, you might need to change some paths in the script, which can be done in the define paths section of the code.

Dependencies

• FASTQC v0.11.9 or later
• BBMap v38.87 or later
• Trimmomatic v0.39 or later
• BWA v0.7.17 or later
• SAMTools v1.10 or later
• BCFTools v1.10.2-3 or later
• Sambamba v0.7.1 or later
• Python v3.7 or later
  • pysam v0.16.0.1 or later

Contributors

LaanLab. Department of BioNanoScience, Delft University of Technology

• Leila Iñigo de la Cruz
• Enzo Kingma
• Gregory van Beek

License

This work is licensed under Apache 2.0 . The 2.0 version of the Apache License, approved by the ASF in 2004, helps us achieve our goal of providing reliable and long-lived software products through collaborative open source software development.

Last updated: March 25, 2021