TY - JOUR AU - Bedford, T. AU - Riley, S. AU - Barr, I. G. AU - Broor, S. AU - Chadha, M. AU - Cox, N. J. PY - 2015 DA - 2015// TI - Global circulation patterns of seasonal influenza viruses vary with antigenic drift JO - Nature. VL - 523 UR - https://doi.org/10.1038/nature14460 DO - 10.1038/nature14460 ID - Bedford2015 ER - TY - JOUR AU - Quick, J. AU - Grubaugh, N. D. AU - Pullan, S. T. AU - Claro, I. M. AU - Smith, A. D. AU - Gangavarapu, K. PY - 2017 DA - 2017// TI - Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples JO - Nat Protoc VL - 12 UR - https://doi.org/10.1038/nprot.2017.066 DO - 10.1038/nprot.2017.066 ID - Quick2017 ER - TY - JOUR AU - Grubaugh, N. D. AU - Gangavarapu, K. AU - Quick, J. AU - Matteson, N. L. AU - Jesus, J. G. AU - Main, B. J. PY - 2019 DA - 2019// TI - An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-018-1618-7 DO - 10.1186/s13059-018-1618-7 ID - Grubaugh2019 ER - TY - STD TI - Di Paola N, Sanchez-Lockhart M, Zeng X, Kuhn JH, Palacios G. Viral genomics in Ebola virus research. Nat Rev Microbiol. 2020:1–14. https://doi.org/10.1038/s41579-020-0354-7. ID - ref4 ER - TY - JOUR AU - Wu, F. AU - Zhao, S. AU - Yu, B. AU - Chen, Y. M. AU - Wang, W. AU - Song, Z. G. PY - 2020 DA - 2020// TI - A new coronavirus associated with human respiratory disease in China JO - Nature. VL - 579 UR - https://doi.org/10.1038/s41586-020-2008-3 DO - 10.1038/s41586-020-2008-3 ID - Wu2020 ER - TY - STD TI - Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C. et al, Nextstrain: real-time tracking of pathogen evolution. https://doi.org/10.1093/bioinformatics/bty407. ID - ref6 ER - TY - STD TI - Zhang T, Wu Q, Zhang Z. Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Curr Biol. 2020;30:1346–1351.e2. https://doi.org/10.1016/j.cub.2020.03.022. ID - ref7 ER - TY - JOUR AU - Andersen, K. G. AU - Rambaut, A. AU - Lipkin, W. I. AU - Holmes, E. C. AU - Garry, R. F. PY - 2020 DA - 2020// TI - The proximal origin of SARS-CoV-2 JO - Nat Med VL - 26 UR - https://doi.org/10.1038/s41591-020-0820-9 DO - 10.1038/s41591-020-0820-9 ID - Andersen2020 ER - TY - STD TI - Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang M-L, et al. Cryptic transmission of SARS-CoV-2 in Washington state. Science (80- ). 2020:eabc0523. https://doi.org/10.1126/science.abc0523. ID - ref9 ER - TY - JOUR AU - Zhou, P. AU - Yang, X. L. AU - Wang, X. G. AU - Hu, B. AU - Zhang, L. AU - Zhang, W. PY - 2020 DA - 2020// TI - A pneumonia outbreak associated with a new coronavirus of probable bat origin JO - Nature VL - 579 UR - https://doi.org/10.1038/s41586-020-2012-7 DO - 10.1038/s41586-020-2012-7 ID - Zhou2020 ER - TY - JOUR AU - Metsky, H. C. AU - Siddle, K. J. AU - Gladden-Young, A. AU - Qu, J. AU - Yang, D. K. AU - Brehio, P. PY - 2019 DA - 2019// TI - Capturing sequence diversity in metagenomes with comprehensive and scalable probe design JO - Nat Biotechnol VL - 37 UR - https://doi.org/10.1038/s41587-018-0006-x DO - 10.1038/s41587-018-0006-x ID - Metsky2019 ER - TY - STD TI - Vanaerschot M, Mann SA, Webber JT, Kamm J, Bell SM, Bell J, et al. Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay. bioRxiv. 2020:2020.08.25.265074. https://doi.org/10.1101/2020.08.25.265074. ID - ref12 ER - TY - STD TI - Itokawa K, Sekizuka T, Hashino M, Tanaka R, Kuroda M. A proposal of alternative primers for the ARTIC Network's multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing. bioRxiv. 2020:2020.03.10.985150. https://doi.org/10.1101/2020.03.10.985150. ID - ref13 ER - TY - JOUR AU - Gohl, D. M. AU - Vangay, P. AU - Garbe, J. AU - MacLean, A. AU - Hauge, A. AU - Becker, A. PY - 2016 DA - 2016// TI - Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies JO - Nat Biotechnol VL - 34 UR - https://doi.org/10.1038/nbt.3601 DO - 10.1038/nbt.3601 ID - Gohl2016 ER - TY - STD TI - Harcourt J, Tamin A, Lu X, Kamili S, Sakthivel SK, Murray J, et al. Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with 2019 Novel coronavirus disease, United States. Emerg Infect Dis. 2020;26.1266-73. ID - ref15 ER - TY - JOUR AU - Gohl, D. M. AU - Magli, A. AU - Garbe, J. AU - Becker, A. AU - Johnson, D. M. AU - Anderson, S. PY - 2019 DA - 2019// TI - Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-019-1691-6 DO - 10.1186/s13059-019-1691-6 ID - Gohl2019 ER - TY - STD TI - Paden C, Tao Y, Queen K, Zhang J, Li Y, Uehara A, et al. Rapid, sensitive, full-genome sequencing of severe acute respiratory syndrome coronavirus 2. Emerg Infect Dis. 2020;26. https://doi.org/10.3201/eid2610.201800. ID - ref17 ER - TY - JOUR AU - Nelson, A. C. AU - Auch, B. AU - Schomaker, M. AU - Gohl, D. M. AU - Grady, P. AU - Johnson, D. PY - 2020 DA - 2020// TI - Analytical Validation of a COVID-19 qRT-PCR Detection Assay Using a 384-well Format and Three Extraction Methods JO - bioRxiv VL - 2019 ID - Nelson2020 ER - TY - BOOK AU - Andrews, S. AU - FastQC, A. PY - 2010 DA - 2010// TI - Quality control tool for high throughput sequence data ID - Andrews2010 ER - TY - JOUR AU - Zhang, J. AU - Kobert, K. AU - Flouri, T. AU - Stamatakis, A. PY - 2014 DA - 2014// TI - PEAR: a fast and accurate Illumina paired-end reAd mergeR JO - Bioinformatics. VL - 30 UR - https://doi.org/10.1093/bioinformatics/btt593 DO - 10.1093/bioinformatics/btt593 ID - Zhang2014 ER - TY - STD TI - Li H, Durbin R. Fast and accurate long-read alignment with burrows–wheeler transform. Bioinformatics. 2010;26:589–95. https://doi.org/10.1093/bioinformatics/btp698. ID - ref21 ER -