The Biomedical Sequencing Facility (BSF) is part of the joint Genomics Core Facility of the Medical University of Vienna (MUW) and the Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences (OeAW). The BSF is Austria’s first technology platform dedicated to next-generation sequencing (NGS) in biomedicine and expected to play a catalyzing role for the development of genomic medicine in Vienna and Austria.

This Python library and the accompanying scripts are used for day-to-day analysis of next-generation sequencing data sets. The library consists of two main functions.

The Analysis class and its subclasses implement the logic required for submitting processes on a cluster login node.

The Runnable class and its subclasses implements the logic required to run processes on a cluster compute node via the common bsf_run_runnable script.

General settings for the BSF Python library are configured via a ${HOME}/.bsfpython.ini file in the user's home directory. This file is site-specific and its information allows for automatic discovery of raw (e.g., Illumina run folders) and pre-processed (e.g., de-multiplexed lanes and samples) NGS data. A template file template_bsfpython.ini can be found in the doc subdirectory. The template, which documents the configuration options and provides, as far as possible, sensible default settings, needs copying to ${HOME}/.bsfpython.ini before editing accordingly.

The BSF Analysis is central to the BSF pipeline infrastructure. It encapsulates both, logic and data for a multistep analysis procedure. Specific Analysis objects are available, tailored to recurring tasks.

BSF Analysis objects are initialised and configured via INI configuration files. Templates for these files are again provided in the doc subdirectory, document configuration options and provide, as far as possible, sensible default settings. Generally, only few configuration options need filling in. Most importantly, the location of sample annotation sheets and, depending on the analysis type, sample comparison sheets, need to be specified.

A sample annotation sheet specifies the file system location of NGS reads. For data pre-processed via Illumina CASAVA, a hierarchy of run folders, projects, samples, and paired reads can be automatically discovered. Additional reads can be linked into the system by specifying the exact file system path. Sample annotation sheets also provide grouping of samples that is available to the analysis.

- Type (CASAVA or External)
- ProcessRunFolder
- Project
- Sample
- Reads1
- File1
- Reads2
- File2
- Group

The ChIPSeq analysis aligns each BSF Sample object to the genome sequence via BWA. Regions of interest are then defined by means of the MACS2 peak caller.

In the context of the ChIPSeq analysis, BSF Paired Reads objects of BSF Sample objects are aligned as a pool.

Please see the RNAseq DESeq document.

The RNA-Seq pipeline is based on the Tuxedo suite. NGS reads are aligned with Tophat2 an aligner that implements a splice site model and uses a reference transcriptome as the base. it is based on the Bowtie2 short read aligner.

In the context of the Tuxedo analysis, BSF Sample objects are aligned and assembled into transcriptomes individually. According to a group_replicates configuration option, each BSF Paired Reads object of a BSF Sample object can be processed individually by TopHat and Cufflinks or pooled before alignment. The resulting transcriptome assemblies for each BSF Sample resulting from each BSF Paired Reads object are then merged via Cuffmerge. Cuffdiff then compares the merged assemblies on the basis of the BAM alignments produced by Tophat2.

• Python (The Python Software Foundation)
• R (The R Foundation for Statistical Computing Platform)

• MACS2 (Tao Liu lab at UB and Xiaole Shirley Liu lab at DFCI)
• DiffBind
• Kent Tools
• convert (ImageMagick Studio LLC)

Copyright 2013 - 2020 Michael K. Schuster

Biomedical Sequencing Facility (BSF), part of the joint Genomics Core Facility of the Medical University of Vienna (MUW) and the Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences (OeAW).

This file is part of BSF Python.

BSF Python is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

BSF Python is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with BSF Python. If not, see http://www.gnu.org/licenses/.