Comparison of Short-Read Sequence Aligners Indicates Strengths and Weaknesses for Biologists to Consider by Ryan Musich, Lance Cadle-Davidson, Lance Cadle-Davidson, Michael V. Osier

Subjects: “…short-read sequencing…”
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Metagenomic Sequencing for Identification of Xylella fastidiosa from Leaf Samples by Verónica Román-Reyna, Enora Dupas, Sophie Cesbron, Guido Marchi, Sara Campigli, Mary Ann Hansen, Elizabeth Bush, Melanie Prarat, Katherine Shiplett, Melanie L. Lewis Ivey, Joy Pierzynski, Sally A. Miller, Francesca Peduto Hand, Marie-Agnes Jacques, Jonathan M. Jacobs

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Short paired-end reads trump long single-end reads for expression analysis by Adam H. Freedman, John M. Gaspar, Timothy B. Sackton

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Investigating the dark-side of the genome: a barrier to human disease variant discovery? by Niamh M. Ryan, Aiden Corvin

Subjects: “…Short-read sequencing…”
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Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity by Michael Gerth, Gregory D.D. Hurst

Subjects: “…Short read sequencing…”
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REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats by Egor Dolzhenko, Ben Weisburd, Kristina Ibañez, Indhu-Shree Rajan-Babu, Christine Anyansi, Mark F. Bennett, Kimberley Billingsley, Ashley Carroll, Samuel Clamons, Matt C. Danzi, Viraj Deshpande, Jinhui Ding, Sarah Fazal, Andreas Halman, Bharati Jadhav, Yunjiang Qiu, Phillip A. Richmond, Christopher T. Saunders, Konrad Scheffler, Joke J. F. A. van Vugt, Ramona R. A. J. Zwamborn, Genomics England Research Consortium, Samuel S. Chong, Jan M. Friedman, Arianna Tucci, Heidi L. Rehm, Michael A. Eberle

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Target capture and genome skimming for plant diversity studies by Flávia Fonseca Pezzini, Giada Ferrari, Laura L. Forrest, Michelle L. Hart, Kanae Nishii, Catherine A. Kidner

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Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya by Rachel M. Palinski, Barbara Brito, Frederick R. Jaya, Abraham Sangula, Francis Gakuya, Miranda R. Bertram, Steven J. Pauszek, Ethan J. Hartwig, George R. Smoliga, Vincent Obanda, George P. Omondi, Kimberly VanderWaal, Jonathan Arzt

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Long-Read Sequencing Annotation of the Transcriptome in DNA-PK Inactivated Cells by Liwei Song, Liwei Song, Mengjun Yu, Renjing Jin, Meng Gu, Ziyu Wang, Dailun Hou, Shaofa Xu, Jinghui Wang, Jinghui Wang, Teng Ma

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Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations by Laurie Lecomte, Mariann Árnyasi, Anne‐Laure Ferchaud, Matthew Kent, Sigbjørn Lien, Kristina Stenløkk, Florent Sylvestre, Louis Bernatchez, Claire Mérot

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Illumina Short-Read Sequencing of the Mitogenomes of Novel <i>Scarites subterraneus</i> Isolates Allows for Taxonomic Refinement of the Genus <i>Scarites</i> Fabricius 1775, within... by Elliot C. Kyndt, John A. Kyndt

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Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations by Rebecca T. Miceli, Tzu‐Yi Chen, Yohei Nose, Swapnil Tichkule, Briana Brown, John F. Fullard, Marilyn D. Saulsbury, Simon O. Heyliger, Sacha Gnjatic, Natasha Kyprianou, Carlos Cordon‐Cardo, Susmita Sahoo, Emanuela Taioli, Panos Roussos, Gustavo Stolovitzky, Edgar Gonzalez‐Kozlova, Navneet Dogra

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Neisseria lactamica Y92–1009 complete genome sequence by Anish K. Pandey, David W. Cleary, Jay R. Laver, Martin C. J. Maiden, Xavier Didelot, Andrew Gorringe, Robert C. Read

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Psi-Caller: A Lightweight Short Read-Based Variant Caller With High Speed and Accuracy by Yadong Liu, Tao Jiang, Yan Gao, Bo Liu, Tianyi Zang, Yadong Wang

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Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle by Guilherme B. Neumann, Paula Korkuć, Monika Reißmann, Manuel J. Wolf, Katharina May, Sven König, Gudrun A. Brockmann

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Choosing the most suitable NGS technology to combine with a standardized viral enrichment protocol for obtaining complete avian orthoreovirus genomes from metagenomic samples by Sonsiray Álvarez-Narváez, Sonsiray Álvarez-Narváez, Telvin L. Harrell, Islam Nour, Sujit K. Mohanty, Steven J. Conrad

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Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies by Jacqueline Rehner, Georges Pierre Schmartz, Laura Groeger, Jan Dastbaz, Nicole Ludwig, Matthias Hannig, Stefan Rupf, Berthold Seitz, Elias Flockerzi, Tim Berger, Matthias Christian Reichert, Marcin Krawczyk, Eckart Meese, Christian Herr, Robert Bals, Sören L. Becker, Andreas Keller, Rolf Müller

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A shotgun metagenomics approach to detect and characterize unauthorized genetically modified microorganisms in microbial fermentation products by Florence E. Buytaers, Marie-Alice Fraiture, Bas Berbers, Els Vandermassen, Stefan Hoffman, Nina Papazova, Kevin Vanneste, Kathleen Marchal, Nancy H.C. Roosens, Sigrid C.J. De Keersmaecker

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Precision metagenomics sequencing for food safety: hybrid assembly of Shiga toxin-producing Escherichia coli in enriched agricultural water by Meghan Maguire, Padmini Ramachandran, Sandra Tallent, Mark K. Mammel, Eric W. Brown, Marc W. Allard, Steven M. Musser, Narjol González-Escalona

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Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes by Wei Zhang, Yingdong Li, Yunmeng Chu, Hao Liu, Hongmei Jing, Qianfeng Xia

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