BOL: Related items

chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes

Neel — Fri, 12 Apr 2019 05:30:41 -0500

Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R 'Shiny' applications.

Address of the bookmark: https://cran.r-project.org/web/packages/chromoMap/vignettes/chromoMap.html

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/

Bokeh: An interactive visualization library that targets modern web browsers for presentation

Jit — Fri, 10 Aug 2018 18:43:08 -0500

Bokeh is an interactive visualization library that targets modern web browsers for presentation. Its goal is to provide elegant, concise construction of versatile graphics, and to extend this capability with high-performance interactivity over very large or streaming datasets. Bokeh can help anyone who would like to quickly and easily create interactive plots, dashboards, and data applications.

To get started using Bokeh to make your visualizations, see the User Guide.

To see examples of how you might use Bokeh with your own data, check out the Gallery.

A complete API reference of Bokeh is at Reference Guide.

If you are interested in contributing to Bokeh, or extending the library, see the Developer Guide.

Address of the bookmark: https://bokeh.pydata.org/en/latest/

shinyCircos: an R/Shiny application for interactive creation of Circos plot

Jit — Fri, 07 Feb 2020 03:26:58 -0600

shinyCircos, a graphical user interface for interactive creation of Circos plot. shinyCircos can be easily installed either on computers for personal use or on local or public servers to provide online use to the community. Furthermore, various types of Circos plots could be easily generated and decorated with simple mouse-click.

Tutorial http://shinycircos.ncpgr.cn/shinyCircos_Help_Manual.pdf

Github https://github.com/venyao/shinyCircos

Address of the bookmark: http://150.109.59.144:3838/shinyCircos/

FQC Dashboard: Integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool

Shruti Paniwala — Tue, 10 Nov 2020 01:30:22 -0600

FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The dashboard groups samples in dropdowns for navigation among the data sets, utilizes human-readable configuration files to manipulate the pages and tabs, and is extensible with CSV data.

Address of the bookmark: https://github.com/pnnl/fqc

1mb long DNA with Nanopore technology

Jit — Tue, 19 Dec 2017 18:49:28 -0600

The first continuous DNA read of more than a million bases (>1Mb) has been achieved, using Oxford Nanopore sequencing technology. Congratulations to Martin Smith and collaborators! Read more: http://bit.ly/2j5TNCO

PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead Approach

Rahul Nayak — Tue, 05 Jun 2018 09:57:11 -0500

PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct contig, PERGA uses paired-end reads and different read overlap sizes from O ≥ Omax to Omin to resolve the gaps and branches. Moreover, by constructing a decision model using machine learning approach based on branch features, PERGA can determine the correct extension in 99.7% of cases. PERGA will try to extend the contigs by all feasible nucleotides and determine if these multiple extensions due to sequencing errors or repeats by using looking ahead technology, and it also try to separate the different repeats of nearby genomic regions to make the assembly result more longer and accurate. The simulated E.coli paired-end reads data are generated using GemSim (KE McElroy, F Luciani, T Thomas. Gemsim: General, Error-Model Based Simulator of Next-Generation Sequencing Data. BMC Genomics 2012, 13:74), with coverage 50x, 60x, 100x, read lengths 100-bp, and can be downloaded from https://github.com/zhuxiao/data_PERGA.

Address of the bookmark: https://github.com/hitbio/PERGA

Read Simulators

Abhi — Fri, 30 Sep 2022 06:48:18 -0500

Short Read Simulators

With the popularity of next-generation sequencing (NGS) technologies, many NGS read simulators have been developed. Currently, many of the popular short read simulators are designed to simulate reads mimicking many Illumina, 454 and SOLiD platforms. Listed below are some popular short read simulators. Links to their publications are provided as well.

Long Read Simulators

With the advancements in sequencing technologies, scientists have shown an increasing interest in using third-generation sequencing (TGS) technologies. Currently, many of the popular long read simulators are designed to simulate reads mimicking the two main TGS technologies; (1) Pacific Biosciences (PacBio) and (2) Oxford Nanopore (ONT). Listed below are some of the popular and recently introduced PacBio and ONT simulators. Links to their publications are provided as well.

PacBio Simulators

ONT Simulators

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

Jit — Fri, 05 Jan 2018 04:12:20 -0600

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (http://dx.doi.org/10.1093/bioinformatics/btu392)
is easy to install/run/configure
supports various types of dat
- HiSeq/MiSeq (100-500bp)
- Unitigs
- 454, ...

proovread maps high coverage data to pacbio reads (bwa mem, blasr, daligner) in multiple iterations.

Address of the bookmark: https://github.com/BioInf-Wuerzburg/proovread

SALSA: A tool to scaffold long read assemblies with Hi-C

Jit — Fri, 15 Jun 2018 04:01:15 -0500

This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, first run the following commands: cd SALSA make To run the code, you will need Python 2.7, BOOST libraries and Networkx(version lower than 1.2). If you consider using this tool, please cite our publication which describes the methods used for scaffolding. Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact information. BMC genomics, 18(1), 527. Link Ghurye, J., Rhie, A., Walenz, B.P., Schmitt, A., Selvaraj, S., Pop, M., Phillippy, A.M. and Koren, S., 2018. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. bioRxiv, p.261149 Link For any queries, please either ask on github issue page or send an email to Jay Ghurye (jayg@cs.umd.edu).

Address of the bookmark: https://github.com/machinegun/SALSA