<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37800?offset=40 https://bioinformaticsonline.com/bookmarks/view/38749/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information Sun, 20 Jan 2019 06:34:36 -0600 https://bioinformaticsonline.com/bookmarks/view/38749/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information <![CDATA[ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information]]> ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome. 

Address of the bookmark: https://github.com/shinout/clipcrop

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/40359/minipolish-a-tool-for-racon-polishing-of-miniasm-assemblies Tue, 03 Dec 2019 02:40:54 -0600 https://bioinformaticsonline.com/bookmarks/view/40359/minipolish-a-tool-for-racon-polishing-of-miniasm-assemblies <![CDATA[Minipolish: A tool for Racon polishing of miniasm assemblies]]> Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads.

Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes.

That's where Minipolish comes in. With a single command, it will use Racon to polish up a miniasm assembly, while keeping the assembly in graph form.

It also takes care of some of the other nuances of polishing a miniasm assembly:

  • Adding read depth information to contigs
  • Fixing sequence truncation that can occur in Racon
  • Adding circularising links to circular contigs if not already present (so they display better in Bandage)
  • 'Rotating' circular contigs between polishing rounds to ensure clean circularisation

Address of the bookmark: https://github.com/rrwick/Minipolish

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/40792/haslr-a-tool-for-rapid-genome-assembly-of-long-sequencing-reads Fri, 31 Jan 2020 05:50:15 -0600 https://bioinformaticsonline.com/bookmarks/view/40792/haslr-a-tool-for-rapid-genome-assembly-of-long-sequencing-reads <![CDATA[HASLR: a tool for rapid genome assembly of long sequencing reads]]> HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample. 

Address of the bookmark: https://github.com/vpc-ccg/haslr

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/41920/liftoff-an-accurate-tool-that-maps-annotations-in-gff-or-gtf-between-assemblies Tue, 30 Jun 2020 21:40:52 -0500 https://bioinformaticsonline.com/bookmarks/view/41920/liftoff-an-accurate-tool-that-maps-annotations-in-gff-or-gtf-between-assemblies <![CDATA[Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies]]>  Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a standalone tool that takes two genome assemblies and a reference annotation as input and outputs an annotation of the target genome. 

Address of the bookmark: https://github.com/agshumate/Liftoff

]]> 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/news/view/10810/uk-executive-accused-in-glaxosmithkline-china-probe Wed, 14 May 2014 04:55:42 -0500 https://bioinformaticsonline.com/news/view/10810/uk-executive-accused-in-glaxosmithkline-china-probe <![CDATA[UK executive accused in GlaxoSmithKline China probe]]> Mark Reilly and two other colleagues are also suspected of bribing government officials in Beijing and Shanghai, they said.

Police have handed the case over to prosecutors, officials said.

GSK said it took the allegations "very seriously" and would co-operate with the authorities over the matter.

Chinese authorities announced in July last year that they were investigating GSK, detaining four Chinese GSK executives.

http://www.bbc.com/news/world-asia-china-27403914

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