BOL: Related items

chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.

Jit — Thu, 03 Feb 2022 04:01:55 -0600

chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.

USAGE:

-query: sequence A in fasta format
-db: sequence B in fasta format
-out: output matrix
-kmer Integer: k>1 (default 32) Use 32 for chromosomes and genomes and 16 for small bacteria
-diffuse Integer: z>0 (default 4) Use 4 for everything - if using large plant genomes you can try using 1
-dimension Size of the output matrix and plot. Integer: d>0 (default 1000) Use 1000 for everything that is not full genome size, where 2000 is recommended

Address of the bookmark: https://github.com/estebanpw/chromeister

JBrowse: Embeddable genome browser built completely with JavaScript and HTML5

Jit — Fri, 29 Jun 2018 09:19:56 -0500

JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes and deep-coverage sequencing. Quickly open and view data files on your computer without uploading them to any server. Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi or .idx index), REST, and more. BAM, BigBed, BigWig, and VCF data are displayed directly from chunks of the compressed binary files, no conversion needed. Includes an optional “faceted” track selector (see demo) suitable for large installations with thousands of tracks. Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance. Can run as a stand-alone app on OSX and Windows using the Electron platform Highly extensible plugin architecture, with a large plugin registry of existing examples here https://gmod.github.io/jbrowse-registry https://jbrowse.org/

Address of the bookmark: https://github.com/GMOD/jbrowse

Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.

Jit — Tue, 18 Jun 2019 05:33:04 -0500

Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding sequences.

Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete.

See a recent presentation on Cogent being applied to the Cuttlefish Iso-Seq data.

Cogent preliminary draft paper (updated 2016Dec version), Supplementary

Please see wiki for details on usage.

Address of the bookmark: https://github.com/Magdoll/Cogent

Biological databases !

BioStar — Wed, 12 Feb 2020 01:16:29 -0600

Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

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

Neel — Tue, 30 Nov 2021 23:23:57 -0600

MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads.

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

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

Genomicus: genome browser that enables users to navigate in genomes in several dimensions

Jit — Mon, 28 Feb 2022 23:27:37 -0600

Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Summary statistics of Genomicus version 105.01: (view species tree in pdf or newick)


Number of extant species	200
Number of extant genes	4303993
Number of ancestral species	196
Number of ancestral genes	4624213
Number of ancestral synteny blocks	83342

Address of the bookmark: https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/cgi-bin/search.pl

deepTools

Martin Jones — Sat, 08 Nov 2014 15:02:08 -0600

deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allows the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.

Publicaton: http://nar.oxfordjournals.org/content/early/2014/05/05/nar.gku365.full

Source Code and Wiki: https://github.com/fidelram/deepTools/wiki

Galaxy Tool Shed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools

and example Galaxy workflows: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows

Genome Context Viewer (GCV)

LEGE — Sun, 21 May 2023 19:33:43 -0500

The Genome Context Viewer (GCV) is a web-app that visualizes genomic context data provided by third party services. Specifically, it uses functional annotations as a unit of search and comparison. By adopting a common set of annotations, data-store operators can deploy federated instances of GCV, allowing users to compare genomes from different providers in a single interface.

Address of the bookmark: https://github.com/legumeinfo/gcv

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

Jit — Sat, 07 Sep 2019 10:45:31 -0500

chromoMap provides interactive, configurable and elegant graphics visualization of chromosomes or chromosomal regions allowing users to map chromosome elements (like genes,SNPs etc.) on the chromosome plot.Each chromosome is composed of loci(representing a specific range determined based on chromosome length) that, on hover, shows details about the annotations in that locus range. The plots can be saved as HTML documents that can be shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

Some of the prominent features of the package are:

visualizing polyploidy simultaneously on the same plot.
annotating groups of elements as distinct colors.
creating chromosome heatmaps.
adjusting chromosome range or visualizing chromosome regions such as genes
adding labels to the plot
adding hyperlinks to each element

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

BioCircos.js is an open source interactive Javascript library to interactive display biological data on the web

Jit — Fri, 19 Jan 2018 15:03:51 -0600

BioCircos.js is an open source interactive Javascript library which provides an easy way to interactive display biological data on the web. It implements a raster-based SVG visualization using the open source Javascript framework jquery.js. BioCircos.js is multiplatform and works in all major internet browsers (Internet Explorer, Mozilla Firefox, Google Chrome, Safari, Opera). Its speed is determined by the client’s hardware and internet browser. For smoothest user experience, we recommend Google Chrome.

BioCircos.js provides SNP, CNV, HEATMAP, LINK, LINE, SCATTER, ARC, TEXT, and HISTGRAMmodules to display genome-wide genetic variations (SNPs, CNVs and chromosome rearrangement), gene expression and biomolecule interactions. BioCircos.js also provides BACKGROUND module to display background and axis circles. Tooltips showing detailed information of SVG elements are also provided.

Demo

Address of the bookmark: http://bioinfo.ibp.ac.cn/biocircos/document/index.html