BOL: Related items

Bandage: interactive visualization of de novo genome assemblies

Shruti Paniwala — Mon, 04 Dec 2017 10:09:37 -0600

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage graphical user interface and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone.

Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage.

Address of the bookmark: http://rrwick.github.io/Bandage/

Epiviz: an interactive visualization tool for functional genomics data.

Jit — Mon, 09 Jul 2018 05:27:39 -0500

Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can addd3 visualizations. You can see a video tour here.

https://bioconductor.org/packages/release/bioc/html/epivizr.html

https://github.com/epiviz

https://github.com/epiviz/epiviz

Address of the bookmark: https://epiviz.github.io/

Hawkeye: an interactive visual analytics tool for genome assemblies

Abhimanyu Singh — Tue, 01 Jan 2019 11:56:17 -0600

Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye.

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-3-r34

Address of the bookmark: http://amos.sourceforge.net/wiki/index.php?title=Hawkeye

Leaflet: JavaScript libraries for interactive maps

Jit — Mon, 10 Feb 2020 01:35:07 -0600

Leaflet is one of the most popular open-source JavaScript libraries for interactive maps.

Features

Interactive panning/zooming
Compose maps using arbitrary combinations of:
- Map tiles
- Markers
- Polygons
- Lines
- Popups
- GeoJSON
Create maps right from the R console or RStudio
Embed maps in knitr/R Markdown documents and Shiny apps
Easily render spatial objects from the sp or sf packages, or data frames with latitude/longitude columns
Use map bounds and mouse events to drive Shiny logic
Display maps in non spherical mercator projections
Augment map features using chosen plugins from leaflet plugins repository

https://rstudio.github.io/leaflet/

Address of the bookmark: https://rstudio.github.io/leaflet/

DECIPHER

Anjana — Fri, 30 Sep 2016 09:33:12 -0500

DECIPHER is a software toolset that can be used to maintain, analyze, and decipher large amounts of DNA sequence data. To install DECIPHER, see the Downloads page.

To begin using DECIPHER read the "Getting Started DECIPHERing" tutorial. Refer to the PDF documents below for instructions on how to use DECIPHER for various tasks.

Address of the bookmark: http://decipher.cee.wisc.edu/Documentation.html

CGView - Circular Genome Viewer

Rahul Nayak — Wed, 20 Jun 2018 10:15:57 -0500

CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases. For examples of the various output types, see the CGView gallery. http://wishart.biology.ualberta.ca/cgview/gallery.html http://stothard.afns.ualberta.ca/downloads/CCT/index.html https://www.gview.ca/wiki/GView/WebHome https://server.gview.ca/ http://stothard.afns.ualberta.ca/cgview_server/ Paper https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx081/4037458

Address of the bookmark: http://wishart.biology.ualberta.ca/cgview/

REAPR: a universal tool for genome assembly evaluation

Jitendra Prajapati — Wed, 06 Apr 2016 18:26:31 -0500

REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly.

http://www.sanger.ac.uk/science/tools/reapr

Address of the bookmark: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-5-r47

truvari: Structural variant comparison tool for VCFs

Jit — Tue, 30 Jun 2020 21:30:44 -0500

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

Interactive Market Intelligence

Pranjali Yadav — Mon, 19 Jan 2015 08:20:38 -0600

BioInformatics LLC, a premier research and advisory firm serving the life science industry, has launched groundbreaking, dynamic-data presentation platform, Interactive Market Intelligence— the only cloud-based market research analytics tool for the life science tools industry.

Superior to traditional PDF and PowerPoint reports, Interactive Market Intelligence allows end-users to filter, create and export literally thousands of views of data — all easily obtainable from a set of core metrics that include market, brand, customer and workflow analytics in well-defined segments of the life science market.

The Market for Real-Time PCR is the first in a series of topics to be explored using the Interactive Market Intelligence platform. The primary research analysis is based on a survey of 900+ international scientists performing qPCR in their laboratories.

Key data findings from "The Market for Real-Time PCR": Global market for qPCR in 2015 is estimated to be $3.6B; The average growth in qPCR throughput is expected to be at 9.8% in 2015; 22% of respondents are highly likely to switch primary suppliers of qPCR products; 50% of respondents use pre-designed primer/probe sets.

GMOL: An Interactive Tool for 3D Genome Structure Visualization

Jit — Wed, 21 Mar 2018 12:25:20 -0500

GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.

Address of the bookmark: https://www.nature.com/articles/srep20802