Snakemake—a scalable bioinformatics workflow engine von Köster, Johannes, Rahmann, Sven

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Snakemake—a scalable bioinformatics workflow engine von KÖSTER, Johannes, RAHMANN, Sven

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Sustainable data analysis with Snakemake [version 2; peer review: 2 approved] von Mölder, Felix, Jablonski, Kim Philipp, Letcher, Brice, Hall, Michael B, Tomkins-Tinch, Christopher H, Sochat, Vanessa, Forster, Jan, Lee, Soohyun, Twardziok, Sven O, Kanitz, Alexander, Wilm, Andreas, Holtgrewe, Manuel, Rahmann, Sven, Nahnsen, Sven, Köster, Johannes

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Rust-Bio: a fast and safe bioinformatics library von Koster, Johannes

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SimLoRD: Simulation of Long Read Data von Stöcker, Bianca K, Köster, Johannes, Rahmann, Sven

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Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing von Uzuner, Hamdiye, Paschen, Annette, Schadendorf, Dirk, Köster, Johannes

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Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo von Lähnemann, David, Köster, Johannes, Fischer, Ute, Borkhardt, Arndt, McHardy, Alice C., Schönhuth, Alexander

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VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis von Cornwell, MacIntosh, Vangala, Mahesh, Taing, Len, Herbert, Zachary, Köster, Johannes, Li, Bo, Sun, Hanfei, Li, Taiwen, Zhang, Jian, Qiu, Xintao, Pun, Matthew, Jeselsohn, Rinath, Brown, Myles, Liu, X Shirley, Long, Henry W

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Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data von Cormier, Michael J., Belyeu, Jonathan R., Pedersen, Brent S., Brown, Joseph, Köster, Johannes, Quinlan, Aaron R.

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MiR‐137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A von Althoff, Kristina, Beckers, Anneleen, Odersky, Andrea, Mestdagh, Pieter, Köster, Johannes, Bray, Isabella M., Bryan, Kenneth, Vandesompele, Jo, Speleman, Frank, Stallings, Raymond L., Schramm, Alexander, Eggert, Angelika, Sprüssel, Annika, Schulte, Johannes H.

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Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery von Koester, Johannes, Dijkstra, Louis J., Marschall, Tobias, Schoenhuth, Alexander

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CRISPR-DO for genome-wide CRISPR design and optimization von Ma, Jian, Köster, Johannes, Qin, Qian, Hu, Shengen, Li, Wei, Chen, Chenhao, Cao, Qingyi, Wang, Jinzeng, Mei, Shenglin, Liu, Qi, Xu, Han, Liu, Xiaole Shirley

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Targeting the innate immunoreceptor RIG-I overcomes melanoma-intrinsic resistance to T cell immunotherapy von Such, Lina, Zhao, Fang, Liu, Derek, Thier, Beatrice, Le-Trilling, Vu Thuy Khanh, Sucker, Antje, Coch, Christoph, Pieper, Natalia, Howe, Sebastian, Bhat, Hilal, Kalkavan, Halime, Ritter, Cathrin, Brinkhaus, Robin, Ugurel, Selma, Koester, Johannes, Seifert, Ulrike, Dittmer, Ulf, Schuler, Martin, Lang, Karl S., Kufer, Thomas A., Hartmann, Gunther, Becker, Jurgen C., Horn, Susanne, Ferrone, Soldano, Liu, David, Van Allen, Eliezer M., Schadendorf, Dirk, Griewank, Klaus, Trilling, Mirko, Paschen, Annette

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VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments von Cui, Yingbo, Wang, Zihang, Koester, Johannes, Liao, Xiangke, Peng, Shaoliang, Tang, Tao, Huang, Chun, Yang, Canqun

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UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example von Thomas, Alexander, Battenfeld, Thomas, Kraiselburd, Ivana, Anastasiou, Olympia, Dittmer, Ulf, Dörr, Ann-Kathrin, Dörr, Adrian, Elsner, Carina, Gosch, Jule, Le-Trilling, Vu Thuy Khanh, Magin, Simon, Scholtysik, René, Yilmaz, Pelin, Trilling, Mirko, Schöler, Lara, Köster, Johannes, Meyer, Folker

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Next‐generation RNA sequencing reveals differential expression of MYCN target genes and suggests the mTOR pathway as a promising therapy target in MYCN‐amplified neuroblastoma von Schramm, Alexander, Köster, Johannes, Marschall, Tobias, Martin, Marcel, Schwermer, Melanie, Fielitz, Kathrin, Büchel, Gabriele, Barann, Matthias, Esser, Daniela, Rosenstiel, Philip, Rahmann, Sven, Eggert, Angelika, Schulte, Johannes H.

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Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing von Tüns, Alicia Isabell, Hartmann, Till, Magin, Simon, González, Rocío Chamorro, Henssen, Anton George, Rahmann, Sven, Schramm, Alexander, Köster, Johannes

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Pancreatic cancer acquires resistance to MAPK pathway inhibition by clonal expansion and adaptive DNA hypermethylation von Godfrey, Laura K, Forster, Jan, Liffers, Sven-Thorsten, Schröder, Christopher, Köster, Johannes, Henschel, Leonie, Ludwig, Kerstin U, Lähnemann, David, Trajkovic-Arsic, Marija, Behrens, Diana, Scarpa, Aldo, Lawlor, Rita T, Witzke, Kathrin E, Sitek, Barbara, Johnsen, Steven A, Rahmann, Sven, Horsthemke, Bernhard, Zeschnigk, Michael, Siveke, Jens T

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Massively parallel read mapping on GPUs with the q-group index and PEANUT von Köster, Johannes, Rahmann, Sven

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NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling [version 1; peer review: 1 approved wit... von Hanssen, Friederike, Gabernet, Gisela, Smith, Nicholas H., Mertes, Christian, Neogi, Avirup Guha, Brandhoff, Leon, Ossowski, Anna, Altmueller, Janine, Becker, Kerstin, Petzold, Andreas, Sturm, Marc, Stöcker, Tyll, Sivalingam, Sugirthan, Brand, Fabian, Schmid, Axel, Buness, Andreas, Probst, Alexander J., Motameny, Susanne, Köster, Johannes

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