<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36723?offset=570 https://bioinformaticsonline.com/bookmarks/view/36590/digest-in-silico-restriction-digest-of-complete-genomes Mon, 14 May 2018 04:02:52 -0500 https://bioinformaticsonline.com/bookmarks/view/36590/digest-in-silico-restriction-digest-of-complete-genomes <![CDATA[Digest: In silico restriction digest of complete genomes]]> This tool allows to retrieve number of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragments is bellow 50, Pulse Field gel Electrophoresis (PFGE) is simulated.

A tool for restriction digest of longuser's sequences is available.

 

Address of the bookmark: http://insilico.ehu.es/digest/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37572/gtdb-tk-a-toolkit-for-assigning-objective-taxonomic-classifications-to-bacterial-and-archaeal-genomes Wed, 22 Aug 2018 03:21:01 -0500 https://bioinformaticsonline.com/bookmarks/view/37572/gtdb-tk-a-toolkit-for-assigning-objective-taxonomic-classifications-to-bacterial-and-archaeal-genomes <![CDATA[GTDB-Tk: A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.]]> GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is computationally efficient and designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).

GTDB-Tk is under active development and validation. Please independently confirm the GTDB-Tk predictions by manually inspecting the tree and bringing any discrepencies to our attention. Notifications about GTDB-Tk releases will be available through the ACE Twitter account (https://twitter.com/ace_uq).

Address of the bookmark: https://github.com/Ecogenomics/GTDBTk

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/40409/haplotypo-a-variant-calling-pipeline-for-phased-genomes Thu, 19 Dec 2019 07:33:40 -0600 https://bioinformaticsonline.com/bookmarks/view/40409/haplotypo-a-variant-calling-pipeline-for-phased-genomes <![CDATA[HaploTypo: a variant-calling pipeline for phased genomes]]> An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome.

Availability and Implementation

HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image.

Address of the bookmark: https://github.com/gabaldonlab/haplotypo

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41918/phispy-phispy-identifies-prophages-in-bacterial-and-probably-archaeal-genomes Tue, 30 Jun 2020 21:36:19 -0500 https://bioinformaticsonline.com/bookmarks/view/41918/phispy-phispy-identifies-prophages-in-bacterial-and-probably-archaeal-genomes <![CDATA[PhiSpy: PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes]]> PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions.

Initial versions of PhiSpy were written by

Sajia Akhter (sajia@stanford.edu) Edwards Bioinformatics Lab

Improvements, bug fixes, and other changes were made by

Katelyn McNair Edwards Bioinformatics Lab and Przemyslaw Decewicz DEMB at the University of Warsaw

Address of the bookmark: https://github.com/linsalrob/PhiSpy

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44313/orthovenn3-an-integrated-platform-for-exploring-and-visualizing-orthologous-data-across-genomes Tue, 02 May 2023 00:48:28 -0500 https://bioinformaticsonline.com/bookmarks/view/44313/orthovenn3-an-integrated-platform-for-exploring-and-visualizing-orthologous-data-across-genomes <![CDATA[OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes]]> OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users from over 60 countries.

Address of the bookmark: https://orthovenn3.bioinfotoolkits.net/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes Tue, 10 Sep 2024 04:54:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes <![CDATA[NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes]]> NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes 

image

NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats.

https://academic.oup.com/bioinformatics/article/39/3/btad121/7072460

Address of the bookmark: https://github.com/hewm2008/NGenomeSyn

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