Prolonged bacterial carriage and hospital transmission detected by whole genome sequencing surveillance by Alexander J. Sundermann, Marissa P. Griffith, Vatsala Rangachar Srinivasa, Kady Waggle, Graham M. Snyder, Daria Van Tyne, Lora Pless, Lee H. Harrison

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STRScan: targeted profiling of short tandem repeats in whole-genome sequencing data by Haixu Tang, Etienne Nzabarushimana

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Algebraic distribution of segmental duplication lengths in whole-genome sequence self-alignments. by Kun Gao, Jonathan Miller

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Application of whole genome sequence analysis to the study of Mycobacterium tuberculosis in Nunavut, Canada. by Andrea D Tyler, Elaine Randell, Maureen Baikie, Kym Antonation, Debra Janella, Sara Christianson, Gregory J Tyrrell, Morag Graham, Gary Van Domselaar, Meenu K Sharma

“…In this study, we applied mycobacterial interspersed repetitive unit (MIRU) variable number of tandem repeat (VNTR) and whole genome sequencing (WGS) to the analysis of Mycobacterium tuberculosis isolates obtained from Northern communities in the territory of Nunavut. …”
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Genomic prediction with whole-genome sequence data in intensely selected pig lines by Roger Ros-Freixedes, Martin Johnsson, Andrew Whalen, Ching-Yi Chen, Bruno D. Valente, William O. Herring, Gregor Gorjanc, John M. Hickey

“…Abstract Background Early simulations indicated that whole-genome sequence data (WGS) could improve the accuracy of genomic predictions within and across breeds. …”
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Identification of Familial Hodgkin Lymphoma Predisposing Genes Using Whole Genome Sequencing by Aayushi Srivastava, Aayushi Srivastava, Aayushi Srivastava, Aayushi Srivastava, Sara Giangiobbe, Sara Giangiobbe, Abhishek Kumar, Nagarajan Paramasivam, Dagmara Dymerska, Wolfgang Behnisch, Mathias Witzens-Harig, Jan Lubinski, Kari Hemminki, Kari Hemminki, Asta Försti, Asta Försti, Asta Försti, Obul Reddy Bandapalli, Obul Reddy Bandapalli, Obul Reddy Bandapalli, Obul Reddy Bandapalli

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HostSeq: a Canadian whole genome sequencing and clinical data resource by S Yoo, E Garg, LT Elliott, RJ Hung, AR Halevy, JD Brooks, SB Bull, F Gagnon, CMT Greenwood, JF Lawless, AD Paterson, L Sun, MH Zawati, J Lerner-Ellis, RJS Abraham, I Birol, G Bourque, J-M Garant, C Gosselin, J Li, J Whitney, B Thiruvahindrapuram, J-A Herbrick, M Lorenti, MS Reuter, OO Adeoye, S Liu, U Allen, FP Bernier, CM Biggs, AM Cheung, J Cowan, M Herridge, DM Maslove, BP Modi, V Mooser, SK Morris, M Ostrowski, RS Parekh, G Pfeffer, O Suchowersky, J Taher, J Upton, RL Warren, RSM Yeung, N Aziz, SE Turvey, BM Knoppers, M Lathrop, SJM Jones, SW Scherer, LJ Strug

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Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans by Ananyo Choudhury, Michèle Ramsay, Scott Hazelhurst, Shaun Aron, Soraya Bardien, Gerrit Botha, Emile R. Chimusa, Alan Christoffels, Junaid Gamieldien, Mahjoubeh J. Sefid-Dashti, Fourie Joubert, Ayton Meintjes, Nicola Mulder, Raj Ramesar, Jasper Rees, Kathrine Scholtz, Dhriti Sengupta, Himla Soodyall, Philip Venter, Louise Warnich, Michael S. Pepper

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Whole genome sequencing distinguishes between relapse and reinfection in recurrent leprosy cases. by Mariane M A Stefani, Charlotte Avanzi, Samira Bührer-Sékula, Andrej Benjak, Chloé Loiseau, Pushpendra Singh, Maria A A Pontes, Heitor S Gonçalves, Emerith M Hungria, Philippe Busso, Jérémie Piton, Maria I S Silveira, Rossilene Cruz, Antônio Schetinni, Maurício B Costa, Marcos C L Virmond, Suzana M Diorio, Ida M F Dias-Baptista, Patricia S Rosa, Masanori Matsuoka, Maria L F Penna, Stewart T Cole, Gerson O Penna

“…In one case, clear evidence was obtained for reinfection with an unrelated strain whereas in the other two cases, relapse appeared more probable.This is the first report of using M. leprae whole genome sequencing to reveal that treated and cured leprosy patients who remain in endemic areas can be reinfected by another strain. …”
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Enabling multiplexed testing of pooled donor cells through whole-genome sequencing by Yingleong Chan, Ying Kai Chan, Daniel B. Goodman, Xiaoge Guo, Alejandro Chavez, Elaine T. Lim, George M. Church

“…Instead, we take advantage of common single nucleotide polymorphisms, whole-genome sequencing, and an algorithm to calculate the proportions from the sequencing data. …”
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Whole-genome sequencing for surveillance of antimicrobial resistance in Ecuador: present and future implications by William Calero-Cáceres, Nimer Ortuño-Gutiérrez, Temmy Sunyoto, Cícero-Armídio Gomes-Dias, Carlos Bastidas-Caldes, Ma. Soledad Ramírez, Anthony D. Harries

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Whole genome sequence analysis of CPV-2 isolates from 1998 to 2020 by Sajed Sarabandi, Hadi Pourtaghi

“…This study collected 126 whole genome sequences of CPV-2 subtypes with specific collection dates from the NCBI data bank. …”
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Whole genome sequencing of peach (<it>Prunus persica </it>L.) for SNP identification and selection by Ahmad Riaz, Parfitt Dan E, Fass Joseph, Ogundiwin Ebenezer, Dhingra Amit, Gradziel Thomas M, Lin Dawei, Joshi Nikhil A, Martinez-Garcia Pedro J, Crisosto Carlos H

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Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak. by Midori Kato-Maeda, Christine Ho, Ben Passarelli, Niaz Banaei, Jennifer Grinsdale, Laura Flores, Jillian Anderson, Megan Murray, Graham Rose, L Masae Kawamura, Nader Pourmand, Muhammad A Tariq, Sebastien Gagneux, Philip C Hopewell

“…METHOD AND MEASUREMENTS: We included 9 patients with tuberculosis diagnosed during a period of 22 months, from a population-based study of the molecular epidemiology in San Francisco. Whole genome sequencing was performed using Illumina's sequencing by synthesis technology. …”
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Determination of Elizabethkingia Diversity by MALDI-TOF Mass Spectrometry and Whole-Genome Sequencing by Helle Brander Eriksen, Heidi Gumpert, Cecilie Haase Faurholt, Henrik Westh

“…In a hospital-acquired infection with multidrug-resistant Elizabethkingia, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene analysis identified the pathogen as Elizabethkingia miricola. Whole-genome sequencing, genus-level core genome analysis, and in silico DNA-DNA hybridization of 35 Elizabethkingia strains indicated that the species taxonomy should be further explored.…”
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Detection of Antibiotic Resistance Genes in Pseudomonas aeruginosa by Whole Genome Sequencing [Letter] by Idrus HH, Sunarno, Rijal S

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Whole-Genome sequencing and genetic variant analysis of a quarter Horse mare by Doan Ryan, Cohen Noah D, Sawyer Jason, Ghaffari Noushin, Johnson Charlie D, Dindot Scott V

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Whole-Genome Sequencing Reveals Age-Specific Changes in the Human Blood Microbiota by Eun-Ju Lee, Joohon Sung, Hyung-Lae Kim, Han-Na Kim

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Whole-genome sequencing and evolutionary analysis of the wild edible mushroom, Morchella eohespera by Yixin Li, Ting Yang, Jinxia Qiao, Jian Liang, Zhonghu Li, Wei Sa, Qianhan Shang

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Data on whole genome sequencing of extrapulmonary tuberculosis clinical isolates from India by Jayshree Advani, Kusum Sharma, Renu Verma, Oishi Chatterjee, Hitendra S. Solanki, Aman Sharma, Subhash Varma, Manish Modi, Pallab Ray, Megha Sharma, M.S. Dhillion, Akhilesh Pandey, Harsha Gowda, T.S. Keshava Prasad

“…This article describes the whole genome sequencing data from 5 extrapulmonary tuberculosis clinical isolates. …”
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