<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/5731?offset=20 https://bioinformaticsonline.com/bookmarks/view/44628/uncovar-workflow-for-transparent-and-robust-virus-variant-calling-genome-reconstruction-and-lineage-assignment Mon, 05 Aug 2024 23:01:29 -0500 https://bioinformaticsonline.com/bookmarks/view/44628/uncovar-workflow-for-transparent-and-robust-virus-variant-calling-genome-reconstruction-and-lineage-assignment <![CDATA[UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment]]> UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment

  • Using state of the art tools, easily extended for other viruses

  • Tool and database updates for critical components via Conda

  • Built using modern design patterns with Conda and Snakemake

  • Extensible and easy to customize

  • Submission Ready Genomes

  • Customizable reporting with comprehensive visualization

https://ikim-essen.github.io/uncovar/

Github https://github.com/IKIM-Essen/uncovar

 

 

Address of the bookmark: https://ikim-essen.github.io/uncovar/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/41493/coronavirus-resources Wed, 25 Mar 2020 17:11:33 -0500 https://bioinformaticsonline.com/bookmarks/view/41493/coronavirus-resources <![CDATA[Coronavirus Resources !]]> 2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains.

Annotation

https://bigd.big.ac.cn/ncov/variation/annotation

Genome wharehouse 

https://bigd.big.ac.cn/gwh/browse/index

Released Genome

https://bigd.big.ac.cn/ncov/release_genome

Download data 

ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/

Raw data

https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae

Address of the bookmark: https://bigd.big.ac.cn/ncov/about

]]> Neel https://bioinformaticsonline.com/bookmarks/view/43112/calling-variants-in-non-diploid-systems Sat, 26 Jun 2021 15:37:49 -0500 https://bioinformaticsonline.com/bookmarks/view/43112/calling-variants-in-non-diploid-systems <![CDATA[Calling variants in non-diploid systems]]> The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA although the same approaches will work equally good on viral and bacterial genomes (Rebolledo-Jaramillo et al. 2014, Li et al. 2015).

Address of the bookmark: https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html

]]> Neel https://bioinformaticsonline.com/videolist/watch/3918/the-human-genome-project-video-3d-animation-introduction-low Sat, 24 Aug 2013 19:01:19 -0500 https://bioinformaticsonline.com/videolist/watch/3918/the-human-genome-project-video-3d-animation-introduction-low <![CDATA[The Human Genome Project Video 3D Animation Introduction Low)]]> ]]> https://bioinformaticsonline.com/videolist/watch/4763/inner-life-of-a-cell-full-versionmkv Mon, 23 Sep 2013 18:09:41 -0500 https://bioinformaticsonline.com/videolist/watch/4763/inner-life-of-a-cell-full-versionmkv <![CDATA[Inner Life Of A Cell - Full Version.mkv]]> Работа аппарата Гольджи и ЭПС при дифференцировке лейкоцита]]> https://bioinformaticsonline.com/videolist/watch/5582/the-human-microbiome-and-what-we-do-to-it Mon, 14 Oct 2013 16:25:10 -0500 https://bioinformaticsonline.com/videolist/watch/5582/the-human-microbiome-and-what-we-do-to-it <![CDATA[The human microbiome and what we do to it]]>

Did you know that you and I are only 1% human — we've 90 trillion cells which don't belong to us. Yes we are more bacteria than human. Have you ever wondered what it means to be human? It turns out that only a tiny percentage of what you and I are made of is actually human — and we need our non-human bits to survive. This part of us now has a name — it's called our microbiome. But we're doing dreadful things to this hidden majority and it's damaging our health as a result. From the Tonic series produced with the assistance of NPS. For more information visit: http://www.nps.org.au

]]> https://bioinformaticsonline.com/videolist/watch/9298/immunology-in-the-gut-mucosa Mon, 17 Mar 2014 11:10:29 -0500 https://bioinformaticsonline.com/videolist/watch/9298/immunology-in-the-gut-mucosa <![CDATA[Immunology in the Gut Mucosa]]> The gut mucosa hosts the body's largest population of immune cells. Nature Immunology in collaboration with Arkitek Studios have produced an animation unravelling the complexities of mucosal immunology in health and disease. Nature Immunology homepage: http://www.nature.com/ni/index.html Nature has full responsibility for all editorial content, including NatureVideo content. This content is editorially independent of sponsors.]]> https://bioinformaticsonline.com/fun/view/14036/introduction-to-programming-write-short-programs-that-generate-graphics-and-animation Thu, 14 Aug 2014 23:29:04 -0500 https://bioinformaticsonline.com/fun/view/14036/introduction-to-programming-write-short-programs-that-generate-graphics-and-animation <![CDATA[Introduction to programming. Write short programs that generate graphics and animation.]]> Introduction to programming. Write short programs that generate graphics and animation.

http://funprogramming.org/

]]> Ram Yash Pal https://bioinformaticsonline.com/news/view/4408/fourth-branch-of-life Mon, 09 Sep 2013 21:48:37 -0500 https://bioinformaticsonline.com/news/view/4408/fourth-branch-of-life <![CDATA[Fourth Branch of Life]]> Scientist have found the biggest viruses known, pandoraviruses which opened up entirely /completely... new questions questions and raise objections to in science. It even suggesting a fourth domain of life.

The new visrus are about one micron—a thousandth of a millimeter—in length, the newfound genus Pandoravirus dwarfs other viruses, which range in size from about 50 nanometers up to 100 nanometers. A genus is a taxonomic ranking between species and family.

Find  more at @ http://www.nature.com/scitable/blog/viruses101/newly_found_pandoraviruses_hint_at

http://news.nationalgeographic.co.uk/news/2013/07/130718-viruses-pandoraviruses-science-biology-evolution/

 

]]> Jitendra Narayan https://bioinformaticsonline.com/news/view/41562/submit-your-sars-cov-2-sequence-data-to-genbank Thu, 09 Apr 2020 18:28:25 -0500 https://bioinformaticsonline.com/news/view/41562/submit-your-sars-cov-2-sequence-data-to-genbank <![CDATA[Submit your SARS-CoV-2 sequence data to GenBank]]> Submit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page. Submission is simple and streamlined *and* there’s a rapid turnaround. https://submit.ncbi.nlm.nih.gov/sarscov2/
 
Quickly and easily add your SARS-CoV-2 sequence data to the growing public archive with new, special features and support from NCBI. new SARS-CoV-2 sequence submission landing page will help you get started. GenBank submissions are accessioned and released in approximately 1-2 working days, and Sequence Read Archive (SRA) submissions typically processed and released within hours. Submission is simple!
]]> Neel