<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/26993?offset=1490 https://bioinformaticsonline.com/bookmarks/view/41831/merqury-reference-free-quality-and-phasing-assessment-for-genome-assemblies Sat, 06 Jun 2020 05:38:34 -0500 https://bioinformaticsonline.com/bookmarks/view/41831/merqury-reference-free-quality-and-phasing-assessment-for-genome-assemblies <![CDATA[Merqury: reference-free quality and phasing assessment for genome assemblies]]> Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this purpose.

https://github.com/marbl/meryl

Address of the bookmark: https://github.com/marbl/merqury

]]> Jit https://bioinformaticsonline.com/poll/view/14927/which-of-the-following-programming-language-is-best-for-a-bioinformatics-beginner Thu, 04 Sep 2014 07:51:16 -0500 https://bioinformaticsonline.com/poll/view/14927/which-of-the-following-programming-language-is-best-for-a-bioinformatics-beginner <![CDATA[Which of the following programming language is best for a bioinformatics beginner?]]> I will be doing NGS in the course of my research work and I will like to learn a programming language which is compatible with most bioinformatics tools or software. I basically want to do de-novo assembly, map reads, align reads, and expression analysis. Recommendations welcomed. Which languages would you recommend to a student wishing to enter the world of bioinformatics?

]]> Manisha Mishra https://bioinformaticsonline.com/bookmarks/view/38481/arcs-scaffolding-genome-drafts-with-linked-reads Mon, 17 Dec 2018 17:40:28 -0600 https://bioinformaticsonline.com/bookmarks/view/38481/arcs-scaffolding-genome-drafts-with-linked-reads <![CDATA[ARCS: scaffolding genome drafts with linked reads]]> ARCS requires two input files:

  • Draft assembly fasta file
  • Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)

Address of the bookmark: https://github.com/bcgsc/ARCS/

]]> Jit https://bioinformaticsonline.com/opportunity/view/16160/research-scientist-%E2%80%93-bioinformatics-at-sidra-medical-and-research-center Wed, 10 Sep 2014 14:35:35 -0500 <![CDATA[Research Scientist – Bioinformatics at Sidra Medical and Research Center]]> Sidra Medical and Research Center(Doha, Qatar) is looking for talented Research Scientists (Bioinformatics / NGS Data Analysis).

Research Scientists within the Bioinformatics Program are involved in research related to cutting edge genomics and analysis of omics data. The research will utilize concepts, theories and best practices obtained from bioinformatics discipline and applied to biological and other biomedical data for analysis. The role may also involve designing databases, algorithm and/or computation methods for analyzing genomics and other omics data. The scientist will be working closely with the Translational Medicine Program within a state-of-the art research setting.

Please check the details of the opening and apply here: http://careers.sidra.org/sidra/Vacan...acancyID=60181

]]> https://bioinformaticsonline.com/opportunity/view/16472/internship-nipgr Sat, 13 Sep 2014 16:02:35 -0500 <![CDATA[INTERNSHIP @ NIPGR]]> Applications are invited from suitable candidates for six months ‘Training Fellowship' at National Institute of Plant Genome Research (NIPGR).

About National Institute Of Plant Genome Research (NIPGR) http://www.nipgr.res.in/

The National Institute of Plant Genome Research is an autonomous institution supported by the Department of Biotechnology, Government of India. It is committed to make the institute a premier Institution for plant genomic research in the country. It was established to contribute in the achievement of such hopes as a part of national effort for meeting the challenges in the midst of fast pace of international genomic research and grasping of opportunities on long-term basis.

About the Internship:

The selected intern(s) will work in the area of in Bioinformatics under the BTISNET program of DBT in the Distributed Information Sub center (DISC) facility at NIPGR, New Delhi, under the supervision of Dr. Gitanjali Yadav, Scientist, NIPGR.

Who can apply:

Students currently pursuing the final year of Masters Degree (or equivalent) in Bioinformatics/Biotechnology with strong interest in Computational Biology and First class/division throughout academic career may apply.

]]> https://bioinformaticsonline.com/file/view/38886/evaluation-of-genome-assembly-software-based-on-long-reads Fri, 01 Feb 2019 11:55:54 -0600 https://bioinformaticsonline.com/file/view/38886/evaluation-of-genome-assembly-software-based-on-long-reads <![CDATA[Evaluation of genome assembly software based on long reads]]> TGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence diversity. They have also been applied to resequencing analyses, to create detailed maps of structural variations in many species. Also, these new technologies have been used to fill in many of the gaps in the human reference genome.

In this report, we compare and evaluate several genome assembly software based on TSG technology. The experimentation has been performed on 4 reference genomes and the results evaluated with the QUAST software. The 11 software that have been evaluated are: Celera Assembler , Falcon , Miniasm, Newbler , SGA Assembler, Smartdenovo, Abruijn, Ra, DBG2OLC, Spades and Cerulean. The first 8 software use only long reads, while the 3 last software can merge long and short reads

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/16682/java-utilities-for-next-generation-sequencing-by-pierre-lindenbaum Mon, 15 Sep 2014 17:24:49 -0500 https://bioinformaticsonline.com/bookmarks/view/16682/java-utilities-for-next-generation-sequencing-by-pierre-lindenbaum <![CDATA[Java utilities for Next Generation Sequencing by Pierre Lindenbaum]]>

Java utilities for Bioinformatics

Address of the bookmark: https://github.com/lindenb/jvarkit

]]> Robert M Willioms https://bioinformaticsonline.com/bookmarks/view/39450/apollo-first-instantaneous-collaborative-genomic-annotation-editor-available-on-the-web Fri, 31 May 2019 19:55:39 -0500 https://bioinformaticsonline.com/bookmarks/view/39450/apollo-first-instantaneous-collaborative-genomic-annotation-editor-available-on-the-web <![CDATA[Apollo: First instantaneous, collaborative genomic annotation editor available on the Web]]>
  • Apollo is a plug-in for the JBrowse Genome Viewer.
  • In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own configuration of the ‘Information Editor’.
  • History tracking with undo/redo functions is available.
  • Users are able to directly set an annotation to a specific state, choosing from the ‘History’ display.
  • Adding and updating PubMed IDs will prompt users with a publication title to confirm their submission.
  • Gene Ontology (GO) terms are supported and GO ID auto-completion has been incorporated.
  • Users may access a ‘Recent Changes’ page.
  • Help page with Apollo specific content is available.

    • Address of the bookmark: http://genomearchitect.github.io/

    ]]>     Jit     https://bioinformaticsonline.com/opportunity/view/17505/kau-thrissur-biotechbioinformatics-rasrfjrftraineestudentships Fri, 26 Sep 2014 20:07:28 -0500 <![CDATA[KAU Thrissur Biotech/Bioinformatics RA/SRF/JRF/Trainee/Studentships]]> Applications are invited from eligible candidates for the following posts at Bioinformatics Centre (DIC), IT- BT Complex, College of Horticulture, Kerala Agricultural University, Vellanikkara, Thrissur.

    1. Research Associate
    Emoluments*: 14880/- + HRA
    Qualification needed: Ph.D/M.Sc in Bioinformatics or Ph.D/M.Sc in Agriculture or Biotechnology with advanced Diploma in Bioinformatics
    Desirable: 2 year experience in Bioinformatics.

    2 Senior Research Fellow
    Emoluments*: 10230/-
    Qualification needed: M.Sc/ M.tech in Bioinformatics or M.Sc in Agriculture/ Biotechnology with Diploma in Bioinformatics.
    Desirable: One year experience in Bioinformatics

    3 Junior Research Fellow
    Emoluments*: 9300/-
    Qualification needed: M.Sc/ M.tech in Bioinformatics or M.Sc in Agriculture/Biotechnology/Plant Sciences with Diploma in Bioinformatics.

    4 .Trainee/Studentship Bioinformatics
    Emoluments*: 5000/-
    Qualification needed: M.Sc in Bioinformatics with good knowledge of Bioinformatics softwares and tools.

    5 Trainee/ Studentship Biotechnology
    Emoluments*: 5000/-
    Qualification needed: M.Sc in Biotechnology, with working knowledge in tissue culture, molecular markers and cloning of genes.

    Candidates with the required qualifications and experience may give an application in the prescribed format with attested copies of certificates to prove eligibility on or before 30th November 2014. The applications are to be addressed to The Associate Dean, College of Horticulture and send to "Professor & Coordinator, Bioinformatics Centre (DIC), IT-BT Complex, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala 680 656”. The envelope may be superscribed “Application for the post at Bioinformatics Centre”.

    *Emoluments are likely to be revised in 2014-2015

    More at http://www.kaubic.in/downloads/Notification_bic.pdf
    http://www.kaubic.in/downloads/Application%20form.pdf

    ]]>         https://bioinformaticsonline.com/bookmarks/view/40302/simug-a-general-purpose-genome-simulator Thu, 28 Nov 2019 04:33:18 -0600 https://bioinformaticsonline.com/bookmarks/view/40302/simug-a-general-purpose-genome-simulator <![CDATA[simuG: a general-purpose genome simulator]]> Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (single nucleotide polymorphisms, Insertions/Deletions, copy number variants, inversions and translocations) for any organisms (including human). The simplicity and versatility of simuG make it a unique general-purpose genome simulator for a wide-range of simulation-based applications.

    Address of the bookmark: https://github.com/yjx1217/simuG

    ]]>     BioStar