scholarly journals MakeHub: Fully automated generation of UCSC Genome Browser Assembly Hubs

2019 ◽  
Author(s):  
Katharina J. Hoff
Keyword(s):  
Genome Annotation ◽  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Visualization Tool ◽  
Command Line ◽  
The Novel ◽  
Automated Generation ◽  
Genome Visualization ◽  
Command Line Tool ◽  
Tool Assembly

AbstractNovel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics. This audience requires tools that are easy to use. This need had been addressed by several genome annotation tools and pipelines. Visualizing resulting annotation is a crucial step of quality control. The UCSC Genome Browser is a powerful and popular genome visualization tool. Assembly Hubs allow browsing genomes that are hosted locally via already available UCSC Genome Browser servers. The steps for creating custom Assembly Hubs are well documented and the required tools are publicly available. However, the number of steps for creating a novel Assembly Hub is large. In some cases the format of input files needs to be adapted which is a difficult task for scientists without programming background. Here, we describe the novel command line tool MakeHub that generates Assembly Hubs for the UCSC Genome Browser in a fully automated fashion. The pipeline also allows extending previously created Hubs by additional tracks.MakeHub is freely available for download from https://github.com/Gaius-Augustus/[email protected]

scholarly journals SparK: A Publication-quality NGS Visualization Tool

2019 ◽  
Author(s):  
Stefan Kurtenbach ◽  
J. William Harbour
Keyword(s):  
Standard Deviation ◽  
Ucsc Genome Browser ◽  
Genomic Region ◽  
Visualization Tool ◽  
Command Line ◽  
Integrative Genomics ◽  
Rna Seq ◽  
Vector Graphic ◽  
Ngs Data ◽  
Publication Quality

AbstractWhile there are sophisticated resources available for displaying NGS data, including the Integrative Genomics Viewer (IGV) and the UCSC genome browser, exporting regions and assembling figures for publication remains challenging. In particular, customizing track appearance and overlaying track replicates is a manual and time-consuming process. Here, we present SparK, a tool which auto-generates publication-ready, high-resolution, true vector graphic figures from any NGS-based tracks, including RNA-seq, ChIP-seq, and ATAC-seq. Novel functions of SparK include averaging of replicates, plotting standard deviation tracks, and highlighting significantly changed areas. SparK is written in Python 3, making it executable on any major OS platform. Using command line prompts to generate figures allows later changes to be made very easy. For instance, if the genomic region of the plot needs to be changed, or tracks need to be added or removed, the figure can easily be re-generated within seconds without the manual process of re-exporting and re-assembling everything. After plotting with SparK, changes to the output SVG vector graphic files are simple to make, including text, lines, and colors. SparK is publicly available on GitHub: https://github.com/harbourlab/SparK.

scholarly journals The UCSC Genome Browser database: 2018 update

2017 ◽  
Vol 46 (D1) ◽  
pp. D762-D769 ◽  
Author(s):  
Jonathan Casper ◽  
Ann S Zweig ◽  
Chris Villarreal ◽  
Cath Tyner ◽  
Matthew L Speir ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Gene Interactions ◽  
Command Line ◽  
Web Interface ◽  
Variant Annotation ◽  
The Past ◽  
Ucsc Genome Browser Database ◽  
Genome Assemblies ◽  
Command Line Version

Abstract The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis—12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.

scholarly journals Visualization of circular RNAs and their internal splicing events from transcriptomic data

2020 ◽  
Vol 36 (9) ◽  
pp. 2934-2935 ◽  
Author(s):  
Yi Zheng ◽  
Fangqing Zhao
Keyword(s):  
Supplementary Information ◽  
Circular Rnas ◽  
Visualization Tool ◽  
Command Line ◽  
Supplementary Data ◽  
Transcriptomic Data ◽  
Command Line Tool ◽  
Transcriptome Comparison ◽  
Multiple Samples ◽  
Splicing Patterns

Abstract Summary Circular RNAs (circRNAs) are proved to have unique compositions and splicing events distinct from canonical mRNAs. However, there is no visualization tool designed for the exploration of complex splicing patterns in circRNA transcriptomes. Here, we present CIRI-vis, a Java command-line tool for quantifying and visualizing circRNAs by integrating the alignments and junctions of circular transcripts. CIRI-vis can be applied to visualize the internal structure and isoform abundance of circRNAs and perform circRNA transcriptome comparison across multiple samples. Availability and implementation https://sourceforge.net/projects/ciri/files/CIRI-vis. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals LAVA: a streamlined visualization tool for longitudinal analysis of viral alleles

2019 ◽  
Author(s):  
Michelle J. Lin ◽  
Ryan C. Shean ◽  
Negar Makhsous ◽  
Alexander L. Greninger
Keyword(s):  
Genome Evolution ◽  
Longitudinal Analysis ◽  
Viral Evolution ◽  
Read Depth ◽  
Visualization Tool ◽  
Command Line ◽  
Interactive Analysis ◽  
Command Line Tool ◽  
User Friendly ◽  
Over Time

AbstractWith their small genomes, fast evolutionary rates, and clinical significance, viruses have long been fodder for studies of whole genome evolution. One common need in these studies is the analysis of viral evolution over time through longitudinal sampling. However, there exists no simple tool to automate such analyses. We created a simple command-line visualization tool called LAVA (Longitudinal Analysis of Viral Alleles). LAVA allows dynamic and interactive visualization of viral evolution across the genome and over time. Results are easily shared via a single HTML file that also allows interactive analysis based on read depth and allele frequency. LAVA requires minimal input and runs in minutes for most use cases. LAVA is programmed mainly in Python 3 and is compatible with Mac and Linux machines. LAVA is a user-friendly command-line tool for generating, visualizing, and sharing the results of longitudinal viral genome evolution analysis. Instructions for downloading, installing, and using LAVA can be found at https://github.com/michellejlin/lava.

scholarly journals Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files

2015 ◽  
Vol 14 ◽  
pp. CIN.S26470 ◽  
Author(s):  
Richard P. Finney ◽  
Qing-Rong Chen ◽  
Cu V. Nguyen ◽  
Chih Hao Hsu ◽  
Chunhua Yan ◽  
...  
Keyword(s):  
Graphical User Interface ◽  
Reference Genome ◽  
Source Code ◽  
Software Tool ◽  
Command Line ◽  
Sequencing Data ◽  
Genome Data ◽  
Command Line Tool ◽  
Portable Software ◽  
Microsoft Windows

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview . The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview .

scholarly journals FAN-C: A Feature-rich Framework for the Analysis and Visualisation of C data

2020 ◽  
Author(s):  
Kai Kruse ◽  
Clemens B. Hug ◽  
Juan M. Vaquerizas
Keyword(s):  
High Throughput ◽  
Matrix Analysis ◽  
Set Covering ◽  
Command Line ◽  
Chromosome Conformation ◽  
C Storage ◽  
Data Formats ◽  
Analysis Tools ◽  
Command Line Tool ◽  
Broad Feature

Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C and its derivatives, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we present FAN-C, an easy-to-use command-line tool and powerful Python API with a broad feature set covering matrix generation, analysis, and visualisation for C-like data (https://github.com/vaquerizaslab/fanc). Due to its comprehensiveness and compatibility with the most prevalent Hi-C storage formats, FAN-C can be used in combination with a large number of existing analysis tools, thus greatly simplifying Hi-C matrix analysis.

Comparative Genomic Analysis Using the UCSC Genome Browser

2007 ◽  
pp. 17-34 ◽  
Author(s):  
Donna Karolchik ◽  
Gill Bejerano ◽  
Angie S. Hinrichs ◽  
Robert M. Kuhn ◽  
Webb Miller ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genome Browser ◽  
Comparative Genomic

scholarly journals ScaffoldGraph: an open-source library for the generation and analysis of molecular scaffold networks and scaffold trees

2020 ◽  
Vol 36 (12) ◽  
pp. 3930-3931 ◽  
Author(s):  
Oliver B Scott ◽  
A W Edith Chan
Keyword(s):  
Open Source ◽  
High Throughput Screening ◽  
Chemical Space ◽  
Diversity Analysis ◽  
Graph Analysis ◽  
Command Line ◽  
Molecular Scaffold ◽  
Large Sets ◽  
Command Line Tool ◽  
Scaffold Diversity

Abstract Summary ScaffoldGraph (SG) is an open-source Python library and command-line tool for the generation and analysis of molecular scaffold networks and trees, with the capability of processing large sets of input molecules. With the increase in high-throughput screening data, scaffold graphs have proven useful for the navigation and analysis of chemical space, being used for visualization, clustering, scaffold-diversity analysis and active-series identification. Built on RDKit and NetworkX, SG integrates scaffold graph analysis into the growing scientific/cheminformatics Python stack, increasing the flexibility and extendibility of the tool compared to existing software. Availability and implementation SG is freely available and released under the MIT licence at https://github.com/UCLCheminformatics/ScaffoldGraph.

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