<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36635?offset=630 https://bioinformaticsonline.com/bookmarks/view/38579/genomeview-genome-browser-and-annotation-editor Wed, 02 Jan 2019 04:09:06 -0600 https://bioinformaticsonline.com/bookmarks/view/38579/genomeview-genome-browser-and-annotation-editor <![CDATA[GenomeView: genome browser and annotation editor]]> GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.
This project has moved to GitHub: https://github.com/GenomeView/genomeview

Address of the bookmark: https://sourceforge.net/projects/genomeview/

]]> Rahul Nayak https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assembly Tue, 22 Jan 2019 09:39:02 -0600 https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assembly <![CDATA[List of tools frequently used while genome assembly]]> List of tools frequently used while genome assembly:

I have used the following assemblers

I have used the following mappers

I have used the following polishing tools

I have used the following tools to assess genome assembly characteristics

If you have any ideas or superior tools we have missed please let us know in the comments.

]]> BioStar https://bioinformaticsonline.com/researchlabs/view/39704/the-rogers-lab Mon, 15 Jul 2019 08:07:44 -0500 <![CDATA[The Rogers Lab]]> The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for adaptation. We are currently working on projects in Drosophila, Mammoths, Elephants, Bivalves, and Frogs absolutely no amphibians. This multi-organism approach can help us understand when and why complex mutations are important for organism fitness.

More at http://evolscientist.com/

]]> https://bioinformaticsonline.com/bookmarks/view/40302/simug-a-general-purpose-genome-simulator Thu, 28 Nov 2019 04:33:18 -0600 https://bioinformaticsonline.com/bookmarks/view/40302/simug-a-general-purpose-genome-simulator <![CDATA[simuG: a general-purpose genome simulator]]> Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (single nucleotide polymorphisms, Insertions/Deletions, copy number variants, inversions and translocations) for any organisms (including human). The simplicity and versatility of simuG make it a unique general-purpose genome simulator for a wide-range of simulation-based applications.

Address of the bookmark: https://github.com/yjx1217/simuG

]]> BioStar https://bioinformaticsonline.com/researchlabs/view/40881/liu-lab Tue, 04 Feb 2020 06:27:02 -0600 <![CDATA[Liu Lab]]> Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.

https://liulab-dfci.github.io/software/

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