<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27216?offset=1160 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/opportunity/view/12218/assistant-professor-in-medical-bioinformatics Tue, 24 Jun 2014 01:46:36 -0500 <![CDATA[Assistant Professor in Medical Bioinformatics]]> Advt. No : ME-I/A-IV/03/14
No.of Posts:01 (SC)
Pay Scale:
Pay Band of Rs.15600-39100 + Rs.6000/- GP +NPA @ 25% of Basic Pay +Learning Resource Allowance @ Rs.20,000/-P.A.+ Conveyance Allowance @ Rs. 1650/-P.M.+ Academic Allowance @ Rs.2500/- P.M. and other admissible allowances.
Qualifications:
Area of Specialization:-
Bioinformatics/Computational/Biology/Genomics/ Proteomics/ Structural Biology
1. Postgraduate qualification, e.g. Master’s Degree in Biotechnology/Bioinformatics/ Biophysics.
2. A Doctorate Degree of recognized University/Institute in a basic or allied Medical Science subject e.g. Medical Biotechnology/Biophysics. Bioinformatics/X-ray Crystallography/
Immunology/Structural Biology etc
Experience:
1.Minimum three years teaching and/or research experience in a recognized medical/research Institution in an allied medical subject after obtaining doctorate degree and preferably in Medical
Molecular Biology/ Biophysics/Structural Biology/Genomics and Clinical Proteomics/Computational Biology.
2. Minimum two publication with atleast one in international journal and atleast one as first author
Desirable:-
Consistently excellent scholastic/academic record, demonstrated ability to write grant proposal/(s) successfully, Post Doctoral training in a frontier area of medical Bioinformatics Research and of direct relevance to clinical diagnosis or patient care (preferably from a recognized top-ranking medical institution abroad)
Send your applications to O/O, Deputy Registrar, Recruitment & Establishment Cell, University of Health Sciences, Rohtak by 08.7.2014
For more details,please visit website: http://pgimsrohtak.nic.in/2014%20AP%20Advt.pdf
Last Apply Date: 08 Jul 2014

]]> 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/opportunity/view/12582/postdoc-position-at-centre-mediterraneen-de-medecine-moleculaire Sun, 06 Jul 2014 11:23:06 -0500 <![CDATA[Postdoc position at Centre Méditerranéen de Médecine Moléculaire]]> The research group of Dr. Michele Trabucchi at the Centre Méditerranéen de Médecine Moléculaire (C3M) at INSERM U1065 (University of Nice Sophia-Antipolis, France) is seeking candidates for a Postdoctoral fellow position to start on October 2014 for 3 years funded by FRM (Fondation pour la Recherche Médicale).
The broad interest of the lab is in understanding the expression control and function of small RNAs in activated myeloid cells (visit our webpage to check research interests and publications of the group : http://www.unice.fr/c3m/EN/Equipe10.html ).

The work will focus on the functional studies of small RNAs by using next-generation sequencing approaches.

Candidates should hold a Ph.D. degree and have strong background in bioinformatics.
The University of Nice Sophia-Antipolis provides a wide range of facilities and training essential for biomedical research.
Interested applicants should send a PDF with a cover letter stating research interests and qualifications, an updated CV, a summary of previous research experience and contact information for two references to Michele Trabucchi ( mtrabucchi@unice.fr )

]]> 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/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/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/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/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/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/

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