The nf-core framework for community-curated bioinformatics pipelines von Ewels, Philip A., Peltzer, Alexander, Fillinger, Sven, Patel, Harshil, Alneberg, Johannes, Wilm, Andreas, Garcia, Maxime Ulysse, Di Tommaso, Paolo, Nahnsen, Sven

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Fast and sensitive mapping of nanopore sequencing reads with GraphMap von Sović, Ivan, Šikić, Mile, Wilm, Andreas, Fenlon, Shannon Nicole, Chen, Swaine, Nagarajan, Niranjan

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LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets von Wilm, Andreas, Aw, Pauline Poh Kim, Bertrand, Denis, Yeo, Grace Hui Ting, Ong, Swee Hoe, Wong, Chang Hua, Khor, Chiea Chuen, Petric, Rosemary, Hibberd, Martin Lloyd, Nagarajan, Niranjan

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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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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega von Sievers, Fabian, Wilm, Andreas, Dineen, David, Gibson, Toby J, Karplus, Kevin, Li, Weizhong, Lopez, Rodrigo, McWilliam, Hamish, Remmert, Michael, Söding, Johannes, Thompson, Julie D, Higgins, Desmond G

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Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls von Wang, Shanquan, Chng, Kern Rei, Wilm, Andreas, Zhao, Siyan, Yang, Kun-Lin, Nagarajan, Niranjan, He, Jianzhong

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Structure mapping of dengue and Zika viruses reveals functional long-range interactions von Huber, Roland G., Lim, Xin Ni, Ng, Wy Ching, Sim, Adelene Y. L., Poh, Hui Xian, Shen, Yang, Lim, Su Ying, Sundstrom, Karin B., Sun, Xuyang, Aw, Jong Ghut, Too, Horng Khit, Boey, Peng Hee, Wilm, Andreas, Chawla, Tanu, Choy, Milly M., Jiang, Lu, de Sessions, Paola Florez, Loh, Xian Jun, Alonso, Sylvie, Hibberd, Martin, Nagarajan, Niranjan, Ooi, Eng Eong, Bond, Peter J., Sessions, October M., Wan, Yue

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Making automated multiple alignments of very large numbers of protein sequences von Sievers, Fabian, Dineen, David, Wilm, Andreas, Higgins, Desmond G

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Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences von Ong, Swee Hoe, Kukkillaya, Vinutha Uppoor, Wilm, Andreas, Lay, Christophe, Ho, Eliza Xin Pei, Low, Louie, Hibberd, Martin Lloyd, Nagarajan, Niranjan

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In-depth analysis of human virus-specific CD8+ T cells delineates unique phenotypic signatures for T cell specificity prediction von Schmidt, Florian, Fields, Hannah F., Purwanti, Yovita, Milojkovic, Ana, Salim, Syazwani, Wu, Kan Xing, Simoni, Yannick, Vitiello, Antonella, MacLeod, Daniel T., Nardin, Alessandra, Newell, Evan W., Fink, Katja, Wilm, Andreas, Fehlings, Michael

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Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission von Sim, Shuzhen, Aw, Pauline P K, Wilm, Andreas, Teoh, Garrett, Hue, Kien Duong Thi, Nguyen, Nguyet Minh, Nagarajan, Niranjan, Simmons, Cameron P, Hibberd, Martin L

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Human pharyngeal microbiota in age-related macular degeneration von Ho, Eliza Xin Pei, Cheung, Chui Ming Gemmy, Sim, Shuzhen, Chu, Collins Wenhan, Wilm, Andreas, Lin, Clarabelle Bitong, Mathur, Ranjana, Wong, Doric, Chan, Choi Mun, Bhagarva, Mayuri, Laude, Augustinus, Lim, Tock Han, Wong, Tien Yin, Cheng, Ching Yu, Davila, Sonia, Hibberd, Martin

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Sequence embedding for fast construction of guide trees for multiple sequence alignment von Blackshields, Gordon, Sievers, Fabian, Shi, Weifeng, Wilm, Andreas, Higgins, Desmond G

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An enhanced RNA alignment benchmark for sequence alignment programs von Wilm, Andreas, Mainz, Indra, Steger, Gerhard

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Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints von Sessions, October M, Wilm, Andreas, Kamaraj, Uma Sangumathi, Choy, Milly M, Chow, Angelia, Chong, Yuwen, Ong, Xin Mei, Nagarajan, Niranjan, Cook, Alex R, Ooi, Eng Eong

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Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma von Chng, Kern Rei, Chan, Sock Hoai, Ng, Amanda Hui Qi, Li, Chenhao, Jusakul, Apinya, Bertrand, Denis, Wilm, Andreas, Choo, Su Pin, Tan, Damien Meng Yew, Lim, Kiat Hon, Soetinko, Roy, Ong, Choon Kiat, Duda, Dan G., Dima, Simona, Popescu, Irinel, Wongkham, Chaisiri, Feng, Zhu, Yeoh, Khay Guan, Teh, Bin Tean, Yongvanit, Puangrat, Wongkham, Sopit, Bhudhisawasdi, Vajaraphongsa, Khuntikeo, Narong, Tan, Patrick, Pairojkul, Chawalit, Ngeow, Joanne, Nagarajan, Niranjan

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Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers von Wratten, Laura, Wilm, Andreas, Göke, Jonathan

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StrAl: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time von Dalli, Deniz, Wilm, Andreas, Mainz, Indra, Steger, Gerhard

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Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history von Zhu, Yuan O, Aw, Pauline P K, de Sessions, Paola Florez, Hong, Shuzhen, See, Lee Xian, Hong, Lewis Z, Wilm, Andreas, Li, Chen Hao, Hue, Stephane, Lim, Seng Gee, Nagarajan, Niranjan, Burkholder, William F, Hibberd, Martin

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ConStruct: Improved construction of RNA consensus structures von Wilm, Andreas, Linnenbrink, Kornelia, Steger, Gerhard

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