BOL: Related items

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

Comparative genomics visualisation tools !

Neel — Thu, 17 Feb 2022 05:37:55 -0600

Comparative genomics visualisation tools !

Address of the bookmark: https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&selected=%23BRIG&tag=Comparative

ABACAS

Surabhi Chaudhary — Thu, 16 Feb 2017 12:15:55 -0600

ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly contigs against the reference. The output is then processed to generate a pseudomolecule taking overlaping contigs and gaps in to account. MUMmer's alignment generating programs, Nucmer and Promer are used followed by the 'delta-filter' utility function. Users could also run tblastx on contigs that are not used to generate the pseudomolecule.

Address of the bookmark: http://abacas.sourceforge.net/Manual.html#9._Colour_code

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

LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)

Jit — Mon, 14 May 2018 04:26:30 -0500

LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly.

Further information about LACHESIS, including source code, documentation and a user's guide are available at: http://shendurelab.github.io/LACHESIS.

Manuscript describing LACHESIS was published as: Burton JN#, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology 2013 Dec;31(12):1119-25. doi: 10.1038/nbt.272. PubMed PMID: 24185095.

http://shendurelab.github.io/LACHESIS/

Address of the bookmark: http://shendurelab.github.io/LACHESIS/

ASAR: Advanced metagenomic Sequence Analysis in R

Jit — Mon, 09 Jul 2018 05:20:50 -0500

An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

Job offer for a postdoctoral researcher in genomics / bioinformatics (2 years)

Fri, 22 Oct 2021 04:44:33 -0500

Ongoing research in the group of Karine Van Doninck involves topics at the core of
evolutionary biology, including the evolution of sex, genome maintenance,
recombination and extreme stress resistance on different eukaryotic systems,
including rotifers, amoeba and Corbicula clams. We are employing different tools
(including experimental ecology, population genetics, phylogeny, comparative
genomics, transcriptomics, bioinformatics, molecular and cellular biology) to study
evolutionary processes at the level of populations, both experimental and natural, and
genomes.

Offer
We offer a full-time contract for two years. The contract starts between October 2021
and December 2021. The position involves no or extremely light teaching load, if the
candidate is interested. Salaries are competitive at the European level. The recruited
person will benefit from the Belgian social insurance scheme (health care, etc.) without
additional expenses.

Profile
Applicants are expected to show outstanding commitment to research and must have
obtained a PhD by the start of the position. A strong expertise in genomics is required.
More specifically, solid competences in bioinformatics (e.g. scripting pipelines) and in
genome evolution are needed. Knowledge or interest regarding recombination,
metazoan evolution, phylogenomics and population genomics is an added-value.

Application
Applications should be submitted via email to karine.van.doninck@ulb.be. The
application package should contain the following documents:
- A curriculum vitae with the complete list of publications
- A cover letter mentioning why the candidate is interested in the position
- Minimum 2 recommendation letters
Interviews: Interviews will be conducted with the selected candidates. Selected
candidates could also be invited to give a seminar to MBE ULB.
For any additional information, please contact karine.van.doninck@ulb.be

gggenomes: A grammar of graphics for comparative genomics

Surabhi Chaudhary — Mon, 01 Feb 2021 14:47:32 -0600

gggenomes is a versatile graphics package for comparative genomics. It extends the popular R visualization packageggplot2 by adding dedicated plot functions for genes, syntenic regions, etc. and verbs to manipulate the plot to, for example, quickly zoom in into gene neighborhoods.

Address of the bookmark: https://github.com/thackl/gggenomes

AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome

Jit — Mon, 23 Dec 2019 10:20:13 -0600

We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.

Address of the bookmark: https://github.com/CMU-SAFARI/AirLift

JCVI:Python utility libraries on genome assembly, annotation and comparative genomics

Jit — Tue, 17 Mar 2020 06:19:06 -0500

Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

https://github.com/tanghaibao/jcvi

More at https://github.com/tanghaibao/jcvi/wiki

Address of the bookmark: https://github.com/tanghaibao/jcvi