Welcome to DaisySuite’s documentation!¶
DaisySuite is a mapping-based workflow for analyzing horizontal gene transfer (HGT) events in bacterial data. The Next Generation Sequencing (NGS) input is processed in two major steps.
First, DaisyGPS identifies possible acceptor and donor candidates. Second, Daisy determines exact HGT-regions for the acceptor/donor pairs.
Citation¶
- Trappe, K., Marschall, T., Renard, B.Y. “Detecting horizontal gene transfer by mapping sequencing reads across species boundaries”. Bioinformatics. 2016
- Seiler, E., Trappe, K., Renard, B.Y., Marschall, T. “Where did you come from, where did you go: Enhancing Metagenomic Approaches for Pathogen Identification”. biorxiv. 2018
Tools used¶
- Bioconda: Bioconda website
- Biopython: Cock, P.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B. and de Hoon, M.J.L. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics
- bwa: Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics.
- Conda: Conda website
- Gustaf: Trappe, K., Emde, A., Ehrlich, H., Reinert, K. (2014) Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone. Bioinformatics.
- Laser: Marschall, T. and Schönhuth., A. (2013) LASER: Sensitive Long-Indel-Aware Alignment of Sequencing Reads. arXiv..
- Mason2: Holtgrewe, M. (2010) Mason – A Read Simulator for Second Generation Sequencing Data. Technical Report FU Berlin.
- MicrobeGPS: Lindner, M.S., Renard, B.Y. (2015) Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS. PLoS ONE
- NumPy: van der Walt, S., Colber, S. and Varoquaux, G. (2011) The NumPy Array: A Structure for Efficient Numerical Computation. Computing in Science & Engineering.
- Pandas: McKinney, W. (2010) Data Structures for Statistical Computing in Python. Proceedings of the 9th Python in Science Conference.
- pysam: pysam website
- sak: Github
- samtools: Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics.
- SciPy: Jones, E., Peterson, P., et al. (2001) SciPy: Open Source Scientific Tools for Python
- Snakemake: Köster, J. and Rahmann, S. (2012) Snakemake - scalable bioinformatics workflow engine. Bioinformatics.
- Stellar: Kehr, B., Weese, D., Reiner, K. (2011) STELLAR: fast and exact local alignments. BMC Bioinformatics.
- Yara: Siragusa, E. (2015). Approximate string matching for high-throughput sequencing. PhD Dissertation, Free University of Berlin.