Watchdog is a workflow management system for the automated and distributed analysis of large-scale omics data as generated in DEEP-DV.

The Watchdog software itself is available at: https://github.com/klugem/watchdog

Workflows for omics data analysis are available at: https://github.com/watchdog-wms/watchdog-wms-workflows

Kluge M, Friedel CC. Watchdog – a workflow management system for the distributed analysis of large-scale experimental data. BMC Bioinformatics. Mar 2018. 19(1):97. (»DOI: 10.1186/s12859-018-2107-4.) PDF

Kluge M, Friedl MS, Menzel AL, Friedel CC. Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution. Gigascience. Jun 2020.9(6):giaa068.
(»DOI: 10.1093/gigascience/giaa068) PDF

RegCFinder automatically identifies subregions of genomic input windows (e.g. promoters, genes, enhancers) with differences in read density between two conditions. It can be applied to any type of omics data and thus lends itself to a wide range of applications.

RegCFinder is implemented as a workflow for Watchdog and available at: https://github.com/watchdog-wms/watchdog-wms-workflows

Weiß E, Friedel CC. RegCFinder: targeted discovery of genomic subregions with differential read density. Bioinform Adv. Jul 2023. 3(1):vbad085.
(»DOI: 10.1093/bioadv/vbad085) PDF

ContextMap2 is a splicing-aware read aligner that can be used to map in parallel against multiple genome sequences, including host and viral genomes. It furthermore allows detection of poly(A) sites from sequencing reads, in particular viral poly(A) sites.

ContextMap2 is available at: https://github.com/friedel-lab/ContextMap2

Bonfert T, Csaba G, Zimmer R, Friedel CC. A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinformatics. Apr 2012. 13 Suppl 6(Suppl 6):S9.
(»DOI: 10.1186/1471-2105-13-S6-S9.) PDF

Bonfert T, Csaba G, Zimmer R, Friedel CC. Mining RNA-seq data for infections and contaminations. PLoS One. Sep 2013. 8(9):e73071.
(»DOI: 10.1371/journal.pone.0073071.) PDF

Bonfert T, Kirner E, Csaba G, Zimmer R, Friedel CC. ContextMap 2: fast and accurate context-based RNA-seq mapping. BMC Bioinformatics. Apr 2015. 16:122.
(»DOI: 10.1186/s12859-015-0557-5.) PDF

Bonfert T, Friedel CC. Prediction of Poly(A) Sites by Poly(A) Read Mapping. PLoS One. Jan 2017. 12(1):e0170914.
(»DOI: 10.1371/journal.pone.0170914.) PDF