Simple and Fast Nearest Neighbor Search. - Marcel Birn; Manuel Holtgrewe; Peter Sanders 001; Johannes Singler (ALENEX, 2010)

Engineering a scalable high quality graph partitioner. - Manuel Holtgrewe; Peter Sanders 001; Christian Schulz 003 (IPDPS, 2010)

A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. - Manuel Holtgrewe; Anne-Katrin Emde; David Weese; Knut Reinert (BMC Bioinform., 2011)

RazerS 3: Faster, fully sensitive read mapping. - David Weese; Manuel Holtgrewe; Knut Reinert (Bioinform., 2012)

Fiona: a parallel and automatic strategy for read error correction. - Marcel H. Schulz; David Weese; Manuel Holtgrewe; Viktoria Dimitrova; Sijia Niu; Knut Reinert; Hugues Richard (Bioinform., 2014)

Genome alignment with graph data structures: a comparison. - Birte Kehr; Kathrin Trappe; Manuel Holtgrewe; Knut Reinert (BMC Bioinform., 2014)

Methods for the detection and assembly of novel sequence in high-throughput sequencing data. - Manuel Holtgrewe; Léon Kuchenbecker; Knut Reinert (Bioinform., 2015)

Engineering Algorithms for Personal Genome Pipelines. - Manuel Holtgrewe (2015)

VCFPy: a Python 3 library with good support for both reading and writing VCF. - Manuel Holtgrewe; Dieter Beule (J. Open Source Softw., 2016)

HLA-MA: simple yet powerful matching of samples using HLA typing results. - Clemens Messerschmidt; Manuel Holtgrewe; Dieter Beule (Bioinform., 2017)

AltamISA: a Python API for ISA-Tab files. - Mathias Kuhring; Mikko Nieminen; Jennifer Kirwan; Dieter Beule; Manuel Holtgrewe (J. Open Source Softw., 2019)

DigestiFlow: from BCL to FASTQ with ease. - Manuel Holtgrewe; Clemens Messerschmidt; Mikko Nieminen; Dieter Beule (Bioinform., 2020)

SODAR Core: a Django-based framework for scientific data management and analysis web apps. - Mikko Nieminen; Oliver Stolpe; Franziska Schumann; Manuel Holtgrewe; Dieter Beule (J. Open Source Softw., 2020)

VarFish: comprehensive DNA variant analysis for diagnostics and research. - Manuel Holtgrewe; Oliver Stolpe; Mikko Nieminen; Stefan Mundlos; Alexej Knaus; Uwe Kornak; Dominik Seelow; Lara Segebrecht; Malte Spielmann; Björn Fischer-Zirnsak; Felix Boschann; Ute Scholl; et al. (Nucleic Acids Res., 2020)

Sustainable data analysis with Snakemake. - Felix Mölder; Kim Philipp Jablonski; Brice Letcher; Michael B. Hall; Christopher Tomkins-Tinch; Vanessa V. Sochat; Jan Forster; Soohyun Lee; Sven Twardziok; Alexander Kanitz; Andreas Wilm; Manuel Holtgrewe; et al. (F1000Research, 2021)

ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise. - Vinzenz May; Leonard Koch; Björn Fischer-Zirnsak; Denise Horn; Petra Gehle; Uwe Kornak; Dieter Beule; Manuel Holtgrewe (Bioinform., 2022)