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/

List of visualization tools for genome alignments

Rahul Nayak — Fri, 02 Feb 2018 13:25:33 -0600

Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. But sometime, we need publication ready figure of genomes. Following are the list of genome alignment visualization tools, which could be useful for analysis and interpretation of results:

ABySS Explorer

Interactive Java application that uses a novel graph-based representation to display a sequence assembly and associated metadata

http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer

BamView

Genome browser and annotation tool that allows visualization of sequence features, next-generation sequencing (NGS) data and the results of analyses within the context of the sequence, and also its six-frame translation

http://www.sanger.ac.uk/resources/software/artemis/

DNannotator

Annotation web toolkit for regional genomic sequences

http://bioapp.psych.uic.edu/DNannotator.htm

JVM

Java Visual Mapping tool for NGS reads

http://www.springer.com/cda/content/document/cda_downloaddocument/9789401792448-c2.pdf?SGWID=0-0-45-1487072-p176815501

LookSeq

Web-based visualization of sequences derived from multiple sequencing technologies. Low- or high-depth read pileups and easy visualization of putative single nucleotide and structural variation

http://lookseq.sourceforge.net

MagicViewer

Visualization of short read alignment, identification of genetic variation and association with annotation information of a reference genome

http://bioinformatics.zj.cn/magicviewer/

MapView

Alignments of huge-scale single-end and pair-end short reads

http://omictools.com/mapview-s1367.html

MultiPipMaker

Computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a ‘percent identity plot’ (pip)

http://pipmaker.bx.psu.edu/pipmaker/

PileLineGUI

Handling genome position files in NGS studies

http://sing.ei.uvigo.es/pileline/pilelinegui.html

SAMtools tview

Simple and fast text alignment viewer; NGS compatible

http://www.htslib.org/

SEWAL

Uses a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run

http://www.sourceforge.net/projects/sewal

STAR

A web-based integrated solution to management and visualization of sequencing data

http://wanglab.ucsd.edu/star/browser

SVA

Software for annotating and visualizing sequenced human genomes

http://www.svaproject.org

Viewer (IGV)

Visualization of large heterogeneous datasets, providing a smooth and intuitive user experience at all levels of genome resolution

https://www.broadinstitute.org/igv/

ZOOM Lite

NGS data mapping and visualization software

http://bioinfor.com/zoom/lite/

Genome U-Plot: a whole genome visualization

Rahul Nayak — Fri, 13 Jul 2018 19:50:41 -0500

Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities.

https://github.com/gaitat/GenomeUPlot

Address of the bookmark: https://github.com/gaitat/GenomeUPlot

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

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

Jit — Fri, 24 Jan 2020 04:09:15 -0600

MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization. MitoZ is available from https://github.com/linzhi2013/MitoZ.

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

Tools for Geospatial data analysis !

BioStar — Wed, 22 Mar 2023 02:10:28 -0500

Geospatial data is becoming increasingly important in many fields, including urban planning, environmental science, public health, and more. These tools can help you work with data from a variety of sources, including satellite imagery, GPS data, and other forms of spatial data. They can help you visualize data, perform complex analysis, and even create maps and other visualizations.

The list includes some of the most popular and widely used geospatial tools available in Python. These tools can help you work with data from a variety of sources and in a variety of formats. Some of the tools are focused on visualization, such as Cartopy, Folium, and Contextily, which allow you to create interactive maps and other visualizations. Other tools are more focused on data manipulation and analysis, such as Fiona, GeoPandas, and Rasterio, which allow you to manipulate and analyze spatial data in a variety of ways.

The list also includes some tools for working with specific types of geospatial data. For example, the H3 library is designed specifically for working with hexagonal grids, while PySAL is focused on spatial econometrics and spatial analysis. Whether you are a data scientist, GIS specialist, or geospatial enthusiast, these tools are sure to enhance your work and help you achieve your goals.

In summary, this list is an excellent resource for anyone working with geospatial data in Python. It contains a wide range of tools for working with different types of data, and can help you visualize data, perform complex analysis, and create maps and other visualizations. If you're looking to enhance your skills in geospatial analysis, this list is definitely worth checking out.

These tools are:

ArcGIS - https://lnkd.in/dgC6sKJH
Cartopy - https://lnkd.in/dc8ijXRg
Contextily - https://lnkd.in/dTdQsmKX
Descartes - https://lnkd.in/dCJykxwW
Fiona - https://lnkd.in/d8sJ3Q5a
Folium - https://lnkd.in/dfSsE-MB
GDAL - https://lnkd.in/dYBJBaAY
Geohash - https://lnkd.in/d_NxJ4_M
GeoJSON - https://lnkd.in/daGs2WYq
GeoPandas - https://lnkd.in/dBTFKKV3
Geopy - https://lnkd.in/dfAzR8Xa
Gevent - http://www.gevent.org
H3 - https://h3geo.org/docs/
OSMnx - https://lnkd.in/dm3pHgUS
PyQGIS - https://lnkd.in/dShWyWVr
PySAL - https://pysal.org
Pydeck - https://lnkd.in/dGBFu-iw
Pyproj - https://lnkd.in/dNG9fdkm
RTree - https://lnkd.in/dURMiYpU
Rasterio - https://lnkd.in/dEMC6ve6
Scikit-mobility - https://lnkd.in/dpHhaX2J
Shapely - https://lnkd.in/d568datK

These tools offer a wide range of capabilities for working with geospatial data, from visualizing and manipulating data to performing complex analysis and modeling. Whether you are a data scientist, GIS specialist, or geospatial enthusiast, these tools are sure to enhance your work and help you achieve your goals.

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

LEGE — Tue, 10 Sep 2024 04:54:55 -0500

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

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

Harvest

Jit — Tue, 31 Jan 2017 10:57:56 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15 (11), 1-15 [PDF]

Address of the bookmark: http://harvest.readthedocs.io/en/latest/index.html

J-Circos

Shruti Paniwala — Fri, 17 Feb 2017 09:06:54 -0600

Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the GUI. J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data.

Address of the bookmark: http://www.australianprostatecentre.org/research/software/jcircos

DIAMOND

Jit — Thu, 27 Apr 2017 04:21:54 -0500

DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.

More at file:///home/urbe/Downloads/diamond_manual.pdf

http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3176.html

Address of the bookmark: https://github.com/bbuchfink/diamond