<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36812?offset=410 https://bioinformaticsonline.com/bookmarks/view/41916/truvari-structural-variant-comparison-tool-for-vcfs Tue, 30 Jun 2020 21:30:44 -0500 https://bioinformaticsonline.com/bookmarks/view/41916/truvari-structural-variant-comparison-tool-for-vcfs <![CDATA[truvari: Structural variant comparison tool for VCFs]]> Structural variant comparison tool for VCFs

Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure.

Spiral Genetics

Motivation

Address of the bookmark: https://github.com/spiralgenetics/truvari

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42155/clustergrammer-is-a-web-based-tool-for-visualizing-high-dimensional-data-as-an-interactive-and-shareable-hierarchically-clustered-heatmap Sun, 23 Aug 2020 19:30:17 -0500 https://bioinformaticsonline.com/bookmarks/view/42155/clustergrammer-is-a-web-based-tool-for-visualizing-high-dimensional-data-as-an-interactive-and-shareable-hierarchically-clustered-heatmap <![CDATA[Clustergrammer is a web-based tool for visualizing high-dimensional data as an interactive and shareable hierarchically clustered heatmap]]> Clustergrammer is a web-based tool for visualizing high-dimensional data (e.g. a matrix) as an interactive and shareable hierarchically clustered heatmap. Clustergrammer's front end (Clustergrammer-JS) is built using D3.js and its back-end (Clustergrammer-PY) is built using Python. Clustergrammer produces highly interactive visualizations that enable intuitive exploration of high-dimensional data and has several biology-specific features (e.g. enrichment analysis, see Biology-Specific Features) to facilitate the exploration of gene-level biological data. 

Address of the bookmark: https://github.com/MaayanLab/clustergrammer

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43090/loretta-a-user-friendly-tool-for-assembling-viral-genomes-from-pacbio-sequence-data Wed, 23 Jun 2021 07:54:53 -0500 https://bioinformaticsonline.com/bookmarks/view/43090/loretta-a-user-friendly-tool-for-assembling-viral-genomes-from-pacbio-sequence-data <![CDATA[LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data]]> LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads.

https://academic.oup.com/ve/article/7/1/veab042/6248116

Address of the bookmark: https://academic.oup.com/ve/article/7/1/veab042/6248116

]]> Neel https://bioinformaticsonline.com/bookmarks/view/43867/genomeqc-a-quality-assessment-tool-for-genome-assemblies-and-gene-structure-annotations Thu, 19 May 2022 04:29:05 -0500 https://bioinformaticsonline.com/bookmarks/view/43867/genomeqc-a-quality-assessment-tool-for-genome-assemblies-and-gene-structure-annotations <![CDATA[GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations]]> The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6568-2

Address of the bookmark: https://github.com/HuffordLab/GenomeQC

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44491/cgviewjs-is-a-circular-genome-viewing-tool Wed, 27 Mar 2024 11:16:24 -0500 https://bioinformaticsonline.com/bookmarks/view/44491/cgviewjs-is-a-circular-genome-viewing-tool <![CDATA[CGView.js is a Circular Genome Viewing tool]]> CGView.js is a Circular Genome Viewing tool for visualizing and interacting with small genomes. This software is an adaptation of the Java program CGView.

CGView.js is the genome viewer of Proksee, an expert system for genome assembly, annotation and visualization.

Features

  • Circular and linear views of genomes

  • Capable of drawing genomes up to 10 Mbp with 1000's of features and 100's contigs

  • Smooth zooming down to the sequence level

  • Easily generate features and plots directly form the sequence (e.g. ORFs, GC-content and GC-Skew)

  • Save high resolution PNG maps up to 8000x8000px

  • Fully documented API for interacting with CGView.js maps

Address of the bookmark: https://js.cgview.ca/

]]> LEGE 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

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/40814/accesssyri-finding-genomic-rearrangements-and-local-sequence-differences-from-whole-genome-assemblies Sat, 01 Feb 2020 13:38:49 -0600 https://bioinformaticsonline.com/bookmarks/view/40814/accesssyri-finding-genomic-rearrangements-and-local-sequence-differences-from-whole-genome-assemblies <![CDATA[AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies]]> AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies

SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0

Address of the bookmark: https://github.com/schneebergerlab/syri

]]> Jit https://bioinformaticsonline.com/bookmarks/view/31137/finishersc-a-repeat-aware-and-scalable-tool-for-upgrading-de-novo-assembly-using-long-reads Mon, 27 Feb 2017 09:49:45 -0600 https://bioinformaticsonline.com/bookmarks/view/31137/finishersc-a-repeat-aware-and-scalable-tool-for-upgrading-de-novo-assembly-using-long-reads <![CDATA[FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads]]> FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.

Address of the bookmark: http://kakitone.github.io/finishingTool/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/32190/dbg2olcefficient-assembly-of-large-genomes-using-long-erroneous-reads-of-the-third-generation-sequencing-technologies Wed, 19 Apr 2017 10:09:51 -0500 https://bioinformaticsonline.com/bookmarks/view/32190/dbg2olcefficient-assembly-of-large-genomes-using-long-erroneous-reads-of-the-third-generation-sequencing-technologies <![CDATA[DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies]]> DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

Our work is published in Scientific Reports:

Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci. Rep. 6, 31900; doi: 10.1038/srep31900 (2016).

http://www.nature.com/articles/srep31900

The manual can be downloaded from:

https://github.com/yechengxi/DBG2OLC/raw/master/Manual.docx

To use precompiled versions,please go to:

https://github.com/yechengxi/DBG2OLC/tree/master/compiled

 

Address of the bookmark: https://github.com/yechengxi/DBG2OLC

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35057/ectools-long-read-correction-and-other-correction-tools Fri, 05 Jan 2018 04:02:22 -0600 https://bioinformaticsonline.com/bookmarks/view/35057/ectools-long-read-correction-and-other-correction-tools <![CDATA[ECTOOLS: Long Read Correction and other Correction tools]]> Long Read Correction and other Correction tools

This package is a loose collection of scripts. To run the correction
routine see the section below. Descriptions of the other scripts
are at the bottom of this file.

Contact: gurtowsk@cshl.edu

In short, the correction algorithm takes as input the unitigs from a short read assembly and uses them to correct long read data. More background information for the algorithm can be found:
http://schatzlab.cshl.edu/presentations/2013-06-18.PBUserMeeting.pdf

Address of the bookmark: https://github.com/jgurtowski/ectools

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