- Nov 2022
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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Primers to target the DXS gene24 (one copy per genome) and the ampicillin resistance gene on the plasmid were created using the Primer3Plus design tool
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- Oct 2022
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nanoporetech.com nanoporetech.com
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To perform bacterial genome assembly, we suggest using the third-party de novo assembly tool Flye3. This analysis package represents a complete pipeline, taking raw nanopore reads as input, and producing polished contigs as output. We also recommend one round of polishing with Medaka4. These tools can be found on GitHub
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- Aug 2022
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Varmus, H. (2021, August 31). Covid has revealed the need for genomic sequencing around the world. Financial Times. https://www.ft.com/content/342fd3c3-5a22-49a0-9cef-135f2ccd8700
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twitter.com twitter.com
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ReconfigBehSci. (2021, December 12). RT @ryan_landay: > A new diverse genome has appeared within the B.1.1.529 lineage that has all of the shared mutations of B.1.1.529, some o… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1470066521615605766
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- Jun 2022
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www.frontiersin.org www.frontiersin.org
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whole-genome sequencing (WGS) provides the highest possible subtyping resolution improving the surveillance, outbreak investigation, source attribution, and microbial population studies
Purpose of WGS in population epidemiology
- Surveillance
- Outbreak Investigation
- Source attribution
- Microbial population
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- Mar 2022
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www.thehindu.com www.thehindu.com
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BA.2 sub-lineage has even higher propensity to spread among people and has the ability to infect people who have been fully vaccinated and/or previously infected by escaping from neutralising antibodies induced by vaccination or infection.
Omicron BA2 infects more in vaccinated
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- Feb 2022
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www.nature.com www.nature.com
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Shelton, J. F., Shastri, A. J., Fletez-Brant, K., Stella Aslibekyan, & Auton, A. (2022). The UGT2A1/UGT2A2 locus is associated with COVID-19-related loss of smell or taste. Nature Genetics, 54(2), 121–124. https://doi.org/10.1038/s41588-021-00986-w
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www.nature.com www.nature.com
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Mallapaty, Smriti. ‘Where Did Omicron Come from? Three Key Theories’. Nature 602, no. 7895 (28 January 2022): 26–28. https://doi.org/10.1038/d41586-022-00215-2.
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- Dec 2021
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Genome sequencing is complex, and only 38 laboratories across the country (https://bit.ly/3ED4vrP) have the ability to sequence a virus which is as infectious as this
Viral Genome sequencing facility in India
- 38 labs
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Maxmen, A. (2021). Omicron blindspots: Why it’s hard to track coronavirus variants. Nature. https://doi.org/10.1038/d41586-021-03698-7
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www.theguardian.com www.theguardian.com
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Sridhar, D. (2021, November 28). How bad will the Omicron Covid variant be in Britain? Three things will tell us. The Guardian. https://www.theguardian.com/commentisfree/2021/nov/28/omicron-covid-variant-britain-southern-africa
Tags
- stock market
- immunity
- booster
- science
- South Africa
- vaccine
- England
- government
- vaccine efficacy
- home-testing kit
- public health measures
- mask mandate
- COVID-19
- transmission
- mortality
- lang:en
- travel restrictions
- testing
- UK
- predominant strain
- is:news
- health outcome
- mask wearing
- data
- variant
- protection
- strategy
- Omicron
- hospitalization
- virus genome
- travel ban
Annotators
URL
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- Oct 2021
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www.nature.com www.nature.com
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Mallapaty, S. (2021). The search for people who never get COVID. Nature. https://doi.org/10.1038/d41586-021-02978-6
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www.biorxiv.org www.biorxiv.org
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Rono, E. K. (2021). Covid-19 genomic analysis reveals clusters of emerging sublineages within the delta variant [Preprint]. Genomics. https://doi.org/10.1101/2021.10.08.463334
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- Sep 2021
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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To identify early embryonic base substitutions, we analysed whole-genome sequences of blood samples from 279 individuals with breast cancer (mean sequencing coverage 32-fold; Supplementary Table 1) seeking mutations with VAFs ranging from 10% to 35%
This is what the research is studying.
Tags
Annotators
URL
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www.science.org www.science.org
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Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutierrez, B., Jackson, B., Colquhoun, R., O’Toole, Á., Klein, B., Vespignani, A., COVID-19 Genomics UK (COG-UK) Consortium‡, Volz, E., Faria, N. R., Aanensen, D. M., … Pybus, O. G. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science, 373(6557), 889–895. https://doi.org/10.1126/science.abj0113
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- Aug 2021
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academic.oup.com academic.oup.com
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O’Toole, Á., Scher, E., Underwood, A., Jackson, B., Hill, V., McCrone, J. T., Colquhoun, R., Ruis, C., Abu-Dahab, K., Taylor, B., Yeats, C., du Plessis, L., Maloney, D., Medd, N., Attwood, S. W., Aanensen, D. M., Holmes, E. C., Pybus, O. G., & Rambaut, A. (2021). Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution, veab064. https://doi.org/10.1093/ve/veab064
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- Jul 2021
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science.sciencemag.org science.sciencemag.org
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Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutierrez, B., Jackson, B., Colquhoun, R., O’Toole, Á., Klein, B., Vespignani, A., Consortium‡, T. C.-19 G. U. (CoG-U., Volz, E., Faria, N. R., Aanensen, D., … Pybus, O. G. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science. https://doi.org/10.1126/science.abj0113
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- May 2021
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Mallapaty, S. (2021). India’s neighbours race to sequence genomes as COVID surges. Nature, 593(7860), 485–486. https://doi.org/10.1038/d41586-021-01287-2
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virological.org virological.org
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Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: Preliminary findings - SARS-CoV-2 coronavirus / nCoV-2019 Genomic Epidemiology. (2021, January 25). Virological. https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586/2
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- Apr 2021
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Merrick, J. (2021, April 20). Covid-19 variants: South African strain is causing the most concern for UK scientists. iNews. https://inews.co.uk/news/politics/covid-19-variants-south-african-strain-is-causing-the-most-concern-for-uk-scientists-965679?utm_term=Autofeed&ito=social_itw_theipaper&utm_medium=Social&utm_source=Twitter#Echobox=1618951521
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blogs.bmj.com blogs.bmj.com
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Nabavi, N., & Dobson, J. (2021, April 21). Covid-19 new variants—known unknowns. The BMJ Opinion. https://blogs.bmj.com/bmj/2021/04/21/covid-19-new-variants-known-unknowns/?utm_campaign=shareaholic&utm_medium=twitter&utm_source=socialnetwork
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www.imperial.ac.uk www.imperial.ac.uk
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More transmissible and evasive SARS-CoV-2 variant growing rapidly in Brazil | Imperial News | Imperial College London. (n.d.). Imperial News. Retrieved 18 April 2021, from https://www.imperial.ac.uk/news/216053/more-transmissible-evasive-sarscov2-variant-growing/
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- Mar 2021
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www.krisp.org.za www.krisp.org.za
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de Oliveira T, Lutucuta S, Nkengasong J, Morais J, Paixao JP, Neto Z, Afonso P, Miranda J, David K, Ingles L, Amilton P A P R R C, Freitas H R, Mufinda F, Tessema K S , Tegally H, San E J, Wilkinson E, Giandhari J, Pillay S, Giovanetti M, Naidoo Y, Katzourakis A, Ghafari M, Singh L, Tshiabuila D, Martin D, Lessells R. (2021) A Novel Variant of Interest of SARS-CoV-2 with Multiple Spike Mutations Detected through Travel Surveillance in Africa. medRxiv. https://www.krisp.org.za/publications.php?pubid=330. Accessed 26 March 2021.
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Volz, E., Mishra, S., Chand, M. et al. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature (2021). https://doi.org/10.1038/s41586-021-03470-x
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virological.org virological.org
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Virological. ‘Recombinant SARS-CoV-2 Genomes Involving Lineage B.1.1.7 in the UK - SARS-CoV-2 Coronavirus / SARS-CoV-2 Molecular Evolution’, 17 March 2021. https://virological.org/t/recombinant-sars-cov-2-genomes-involving-lineage-b-1-1-7-in-the-uk/658.
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- Feb 2021
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twitter.com twitter.com
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Miro Weinberger. (2020, December 3). Our 1st Covid-19 wastewater tests since Thanksgiving just came in—Virus levels are up significantly citywide. I hope that all of #BTV will look at this graph and see what I see: A call to action, to stop gathering with other households, and to get tested ASAP if you have https://t.co/8nxTwOOcFA [Tweet]. @MiroBTV. https://twitter.com/MiroBTV/status/1334613511692017664
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www.theguardian.com www.theguardian.com
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Here’s what we know about the new variant of coronavirus | Sharon Peacock. (2020, December 22). The Guardian. http://www.theguardian.com/commentisfree/2020/dec/22/new-variant-coronavirus-genomic-sars-cov-2-pandemic
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- Jan 2021
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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we developed a vastly improved INTEGRATE system that uses streamlined expression vectors to direct highly accurate insertions at ~100% efficiency effectively in a single orientation, independent of the cargo size, without requiring selection markers
Efficiency sounds too exciting to not try!
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- Aug 2020
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medrxiv.org medrxiv.org
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Ferretti, A. P., Kula, T., Wang, Y., Nguyen, D. M., Weinheimer, A., Dunlap, G. S., Xu, Q., Nabilsi, N., Perullo, C. R., Cristofaro, A. W., Whitton, H. J., Virbasius, A., Olivier, K. J., Baiamonte, L. B., Alistar, A. T., Whitman, E. D., Bertino, S. A., Chattopadhyay, S., & MacBeath, G. (2020). COVID-19 Patients Form Memory CD8+ T Cells that Recognize a Small Set of Shared Immunodominant Epitopes in SARS-CoV-2. MedRxiv, 2020.07.24.20161653. https://doi.org/10.1101/2020.07.24.20161653
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www.biorxiv.org www.biorxiv.org
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Guo, L., Boocock, J., Tome, J. M., Chandrasekaran, S., Hilt, E. E., Zhang, Y., Sathe, L., Li, X., Luo, C., Kosuri, S., Shendure, J. A., Arboleda, V. A., Flint, J., Eskin, E., Garner, O. B., Yang, S., Bloom, J. S., Kruglyak, L., & Yin, Y. (2020). Rapid cost-effective viral genome sequencing by V-seq. BioRxiv, 2020.08.15.252510. https://doi.org/10.1101/2020.08.15.252510
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www.youtube.com www.youtube.com
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Science Facebook Live: Understanding SARS-CoV-2 structure informs vaccine design, clinical trials. (2020, March 20). https://www.youtube.com/watch?v=nOzEx3OpKe8
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Qu, J., Cai, Z., Liu, Y., Duan, X., Han, S., Zhu, Y., Jiang, Z., Zhang, Y., Zhuo, C., Liu, Y., Liu, Y., Liu, L., & Yang, L. (2020). Persistent bacterial coinfection of a COVID-19 patient caused by a genetically adapted Pseudomonas aeruginosa chronic colonizer. BioRxiv, 2020.08.05.238998. https://doi.org/10.1101/2020.08.05.238998
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www.medrxiv.org www.medrxiv.org
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Lednicky, J. A., Lauzardo, M., Fan, Z. H., Jutla, A. S., Tilly, T. B., Gangwar, M., Usmani, M., Shankar, S. N., Mohamed, K., Eiguren-Fernandez, A., Stephenson, C. J., Alam, M. M., Elbadry, M. A., Loeb, J. C., Subramaniam, K., Waltzek, T. B., Cherabuddi, K., Morris, J. G., & Wu, C.-Y. (2020). Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients. MedRxiv, 2020.08.03.20167395. https://doi.org/10.1101/2020.08.03.20167395
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www.youtube.com www.youtube.comYouTube1
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LucyinLockdown: Viruses, Pandemics and Lessons Learnt with Dr Jane Greatorex—YouTube. (2020, June 18). https://youtu.be/5U1go5hyen8
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- Jul 2020
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www.nationalgeographic.com www.nationalgeographic.com
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How coronavirus mutations can track its spread—And disprove conspiracies. (2020, March 26). Science. https://www.nationalgeographic.com/science/2020/03/how-coronavirus-mutations-can-track-its-spread-and-disprove-conspiracies/
Tags
- genetics
- lang:en
- misinformation
- transmission
- research
- is:preprint
- genome
- origin
- conspiracy theory
- tracking
- sequencing
- COVID-19
- mutation
Annotators
URL
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www.cell.com www.cell.com
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How scientists know COVID-19 is way deadlier than the flu. (2020, July 2). Science. https://www.nationalgeographic.com/science/2020/07/coronavirus-deadlier-than-many-believed-infection-fatality-rate-cvd/
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www.thelancet.com www.thelancet.com
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Behrmann, Ole, and Martin Spiegel. ‘COVID-19: From Rapid Genome Sequencing to Fast Decisions’. The Lancet Infectious Diseases 0, no. 0 (14 July 2020). https://doi.org/10.1016/S1473-3099(20)30580-6.
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- Jun 2020
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threader.app threader.app
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Balloux, F. (2020, May 22) A thread written by @BallouxFrancois. Threader. https://threader.app/thread/1263745877702737920
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- May 2020
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www.nature.com www.nature.com
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Andersen, K.G., Rambaut, A., Lipkin, W.I. et al. The proximal origin of SARS-CoV-2. Nat Med 26, 450–452 (2020). https://doi.org/10.1038/s41591-020-0820-9
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- Apr 2020
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academic.oup.com academic.oup.com
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"Nala" the female German Shepherd Dog. Nala, or formally “Jonkahra Nala” (Australian Registration #2100398550)
More on Nala in the Vet Candy blog https://www.myvetcandy.com/clinicalupdblog/2020/4/2/first-complete-german-shepherd-dna-offers-new-tool-to-fight-disease
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Findings
Coverage in GenomeWeb https://www.genomeweb.com/scan/german-shepherds-own-sequence#.XoeoXG4o-qA
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- Nov 2017
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www.nature.com www.nature.com
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Two independent modes of chromatin organization revealed by cohesin removal
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Annotators
URL
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- Oct 2017
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www.biostars.org www.biostars.org
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What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
discussion of tools; recently revived
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Annotators
URL
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asciigenome.readthedocs.io asciigenome.readthedocs.io
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ASCIIGenome is a command-line genome browser running from terminal window
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www.sanger.ac.uk www.sanger.ac.uk
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Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation
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Annotators
URL
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github.com github.com
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Genome Maps is a modern and high-performance web-based HTML5 genome browser
Tags
Annotators
URL
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- Sep 2017
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www.biorxiv.org www.biorxiv.org
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Major flaws in "Identification of individuals by trait prediction using whole-genome sequencing data"
re Venter study in PNAS, claiming to be able to identify people based on whole genome data
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www.nature.com www.nature.com
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Plot a course through the genome Inspired by Google Maps, a suite of tools is allowing researchers to chart the complex conformations of chromosomes.
mentioned tools are focused on (capture) Hi-C data
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- Jul 2017
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www.napoleome.ch www.napoleome.ch
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Napoleon oak genome sequencing project web site: example of public engagement in tree genomics
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Annotators
URL
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Quercus robur Genome sequencing and assembly
data (not yet live) associated with https://hyp.is/4DerrmIaEeehDPNBqsRcxQ/www.biorxiv.org/content/biorxiv/early/2017/06/13/149203.full.pdf
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Annotators
URL
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- Jun 2017
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molossinus.lab.nig.ac.jp molossinus.lab.nig.ac.jp
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Takada et al. 2013
NIG Mouse Genome Database: JF1 and MSM SNPs; effective genome browser
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Annotators
URL
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- Sep 2016
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software.broadinstitute.org software.broadinstitute.org
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You must quit IGV and restart for this preference to take effect. The genome should appear in the drop-down list.
restart may be insufficient; had to modify prefs.properties in ~/igv (removing old cached genome values) before i could see my genomes
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- Apr 2016
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gigadb.org gigadb.org
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IsPreviousVersionOf doi:10.5524/100148
This paper was studied in a case study that lead to some corrections. See the paper here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127612
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gigadb.org gigadb.org
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genomically poorly explored
Poorly studied in some part to its very high degree of heterozygosity. You can get some more insight here, where it was nominated as a "top ten genome" http://www.homolog.us/blogs/blog/2015/05/08/top-ten-genomes-ix-pacific-oyster/
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Annotators
URL
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gigadb.org gigadb.org
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Long Fragment Read technology
See Nature doi:10.1038/nature11236 for more on how LFR works: http://www.nature.com/nature/journal/v487/n7406/full/nature11236.html
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Annotators
URL
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