<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/31064?offset=1030 https://bioinformaticsonline.com/bookmarks/view/38166/pygenometracks-standalone-program-and-library-to-plot-beautiful-genome-browser-tracks Fri, 09 Nov 2018 12:34:23 -0600 https://bioinformaticsonline.com/bookmarks/view/38166/pygenometracks-standalone-program-and-library-to-plot-beautiful-genome-browser-tracks <![CDATA[pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks]]> pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:

  • bigwig
  • bed (many options)
  • bedgraph
  • links (represented as arcs)
  • Hi-C matrices (if HiCExplorer is installed)

Address of the bookmark: https://github.com/deeptools/pyGenomeTracks

]]> Neel https://bioinformaticsonline.com/bookmarks/view/38224/novograph-building-whole-genome-graphs-from-long-read-based-de-novo-assemblies Thu, 15 Nov 2018 12:48:30 -0600 https://bioinformaticsonline.com/bookmarks/view/38224/novograph-building-whole-genome-graphs-from-long-read-based-de-novo-assemblies <![CDATA[NovoGraph: building whole genome graphs from long-read-based de novo assemblies]]> NovoGraph: building whole genome graphs from long-read-based de novo assemblies

An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of principle by creating a genome graph of seven ethnically-diverse human genomes.

 

https://f1000research.com/articles/7-1391/v1

Address of the bookmark: https://github.com/NCBI-Hackathons/NovoGraph

]]> Jit https://bioinformaticsonline.com/videolist/watch/14218/pimp-your-brain-bioinformatics Wed, 20 Aug 2014 22:09:21 -0500 https://bioinformaticsonline.com/videolist/watch/14218/pimp-your-brain-bioinformatics <![CDATA[Pimp your brain: Bioinformatics]]> Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformatics is so important and indispensable for biological research. In the video serial "Pimp your brain" scientists from the Max Planck Institute of Molecular Plant Physiology describe their research. More videos from the 'Pimp your brain' serial are available on www.youtube.com/playlist?list=PL-l9VItC9Gn2Ur2Xj6PTOAkjLUlVPbIOO More videos are available on www.mpimp-golm.mpg.de]]> https://bioinformaticsonline.com/bookmarks/view/38475/purge-haplotigs-pipeline-to-help-with-curating-heterozygous-diploid-genome-assemblies Mon, 17 Dec 2018 03:17:20 -0600 https://bioinformaticsonline.com/bookmarks/view/38475/purge-haplotigs-pipeline-to-help-with-curating-heterozygous-diploid-genome-assemblies <![CDATA[Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies]]> Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an issue for downstream analysis whether you're working on the haploid or phased-diploid assembly.

Identify pairs of contigs that are syntenic and move one of them to the haplotig 'pool'. The pipeline uses mapped read coverage and Minimap2 alignments to determine which contigs to keep for the haploid assembly. Dotplots are optionally produced for all flagged contig matches, juxtaposed with read-coverage, to help the user determine the proper assignment of any remaining ambiguous contigs. The pipeline will run on either a haploid assembly (i.e. Canu, FALCON or FALCON-Unzip primary contigs) or on a phased-diploid assembly (i.e. FALCON-Unzip primary contigs + haplotigs). Here are two examples of how Purge Haplotigs can improve a haploid and diploid assembly.

Address of the bookmark: https://bitbucket.org/mroachawri/purge_haplotigs

]]> Rahul Nayak https://bioinformaticsonline.com/researchlabs/view/12989/center-for-molecular-dynamics-nepal-cmdn-nepal Wed, 23 Jul 2014 13:54:51 -0500 <![CDATA[Center for Molecular Dynamics Nepal (CMDN), Nepal]]> Center for Molecular Dynamics Nepal (CMDN), established 2007 prides itself as a research driven nongovernmental organization. Unlike other civil society organizations, CMDN is dedicated entirely to promoting research in the country. With its team of energetic and highly motivated experts, CMDN is now recognized as the leading public health and wildlife research organization of the country.

More at http://www.cmdn.org.np/main/index.php

]]> https://bioinformaticsonline.com/bookmarks/view/38579/genomeview-genome-browser-and-annotation-editor Wed, 02 Jan 2019 04:09:06 -0600 https://bioinformaticsonline.com/bookmarks/view/38579/genomeview-genome-browser-and-annotation-editor <![CDATA[GenomeView: genome browser and annotation editor]]> GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.
This project has moved to GitHub: https://github.com/GenomeView/genomeview

Address of the bookmark: https://sourceforge.net/projects/genomeview/

]]> Rahul Nayak https://bioinformaticsonline.com/videolist/watch/13267/the-genome-10k-project Tue, 29 Jul 2014 09:11:04 -0500 https://bioinformaticsonline.com/videolist/watch/13267/the-genome-10k-project <![CDATA[The Genome 10K Project]]> https://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction in DNA sequencing suggests that this project will be feasible within a few years. Capturing the genetic diversity of vertebrate species would create an unprecedented resource for the life sciences and for worldwide conservation efforts. The growing Genome 10K Community of Scientists (G10KCOS), made up of leading scientists representing major zoos, museums, research centers, and universities around the world, is dedicated to coordinating efforts in tissue specimen collection that will lay the groundwork for a large-scale sequencing and analysis project.]]> https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assembly Tue, 22 Jan 2019 09:39:02 -0600 https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assembly <![CDATA[List of tools frequently used while genome assembly]]> List of tools frequently used while genome assembly:

I have used the following assemblers

I have used the following mappers

I have used the following polishing tools

I have used the following tools to assess genome assembly characteristics

If you have any ideas or superior tools we have missed please let us know in the comments.

]]> BioStar https://bioinformaticsonline.com/opportunity/view/13477/research-associate-at-indian-institute-of-chemical-technology-iict-hyderabad Thu, 07 Aug 2014 01:55:21 -0500 <![CDATA[Research Associate at Indian Institute of Chemical Technology (IICT), Hyderabad]]> Indian Institute of Chemical Technology (IICT), Hyderabad, a constituent of CSIR is a leading research Institute in the area of chemical sciences. The core strength of IICT lies in Organic Chemistry, and it continues to excel in this field for over six decades. The research efforts during these years have resulted in the development of several innovative processes for a variety of products necessary for human welfare such as drugs, agrochemicals, food, organic intermediates, adhesives etc. More than 150 technologies developed by IICT are now in commercial production.

CSIR-IICT is conducting Walk in Interview for the following position on a purely temporary basis for the sponsored project "GENESIS (BSC-0121) at 10.00 AM on 19th August 2014 at IICT, Hyderabad

Position : Research Associate
No of Post : One
Desired Profile : PhD in computation biology or M.Tech in Computational Biology with three years experience in relevant subject and atleast one research paper in SCI journal

Experience : Knowledge in vector and vector borne disease, disease modeling, GIS mapping and modeling.
Age : 35 years
Stipend : Rs 22000/- + HRA

Eligible candidate may download the application form from our website http://www.iictindia.org and appear for interview along with the duly filled in application form supported by bio-data and one set of attested photo copies of certificates of educational qualification, age, experience, caste, latest photograph and the cadndidates are required to bring all the original certificates for verification

Walk in Interview : 19.08.14

]]> https://bioinformaticsonline.com/researchlabs/view/39704/the-rogers-lab Mon, 15 Jul 2019 08:07:44 -0500 <![CDATA[The Rogers Lab]]> The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for adaptation. We are currently working on projects in Drosophila, Mammoths, Elephants, Bivalves, and Frogs absolutely no amphibians. This multi-organism approach can help us understand when and why complex mutations are important for organism fitness.

More at http://evolscientist.com/

]]>