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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27099?offset=540</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44768/tritex-a-computational-pipeline-for-chromosome-scale-assembly-of-plant-genomes</guid>
	<pubDate>Fri, 14 Feb 2025 10:53:48 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44768/tritex-a-computational-pipeline-for-chromosome-scale-assembly-of-plant-genomes</link>
	<title><![CDATA[TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes]]></title>
	<description><![CDATA[<p><span>This is the documentation of TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes. It was developed in the research group Domestication Genomics at the Leibniz Institute of Plant Genetics and Crop Research (IPK) Gatersleben.</span></p><p>Address of the bookmark: <a href="https://tritexassembly.bitbucket.io/" rel="nofollow">https://tritexassembly.bitbucket.io/</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18380/jrfsrf-at-university-of-hyderabad</guid>
  <pubDate>Fri, 17 Oct 2014 01:55:44 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF/SRF at University of Hyderabad]]></title>
  <description><![CDATA[
<p>Applications are invited for the following post of Junior Research Fellow (temporary position coterminous with the project) under DBT funded research project on ““Understanding the functions of α1β1γ1/α2β1γ1 selective AMPK Modulators in dissecting the pharmacological role of these isozymes in metabolic diseases”</p>

<p>Qualified and interested candidates can send their curriculum vitae by e-mail to hr@drils.org on or before 27th October 2014 mention in the subject line of the mail the following code: AMPK-Biology.</p>

<p>Selected candidates will be called for a personal interview to Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad. The selected candidate is expected to report within two weeks from the date of selection to start work on the project.</p>

<p>Junior Research Fellowship (Molecular Modeling/Biology) for two years and Senior Research fellowship for one year</p>

<p>Junior Research Fellowship: Rs. 15,600/- (consolidated) per month for first two years.<br />Senior Research Fellowship: Rs. 18,200/-(consolidated) per month for the 3rd year.</p>

<p>Duration: The duration of the fellowship is for three years. However, the performance of the candidate will be reviewed after the completion of every year and the fellowship will be renewed only upon satisfactory performance.</p>

<p>Responsibilities:</p>

<p>1) Literature search.<br />2) Design, plan and execute experiments under the supervision of the scientist.<br />3) Provide scientific support to the scientist in his/her research activities.<br />4) Book keeping and maintenance of stocks and consumables.</p>

<p>Essential Qualifications:</p>

<p>Required: M.Sc. in Microbiology/Biotechnology/Bioinformatics or any other related branch of basic Sciences from a recognized university/institute with a consistent academic record of minimum 60% aggregate in all qualifying examinations. The candidate should be NET qualified for lectureship. The candidate should be motivated to work with dedication.</p>

<p>Desirable: expertise/experience in both Molecular Modeling and Molecular Biology.</p>

<p>Experience: 0-2 years in the areas of Molecular Modeling and/or Molecular Biology and cell biology and Biochemistry.</p>

<p>Preferable: Relevant research experience as evident from thesis/dissertation/project work.</p>

<p>Advertisement: http://www.ilsresearch.org/userfiles/Junior%20REsearch%20Fellowship%20-%20AMPK(Biology).pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34678/svfinder-tool-for-detecting-genomic-rearrangement-form-dna-seq-data</guid>
	<pubDate>Thu, 14 Dec 2017 15:51:40 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34678/svfinder-tool-for-detecting-genomic-rearrangement-form-dna-seq-data</link>
	<title><![CDATA[SVfinder: Tool for detecting genomic rearrangement form DNA-seq data]]></title>
	<description><![CDATA[<p><span>SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.</span></p><p>Address of the bookmark: <a href="https://github.com/cauyrd/SVfinder" rel="nofollow">https://github.com/cauyrd/SVfinder</a></p>]]></description>
	<dc:creator>Robert M Willioms</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36012/gmol-an-interactive-tool-for-3d-genome-structure-visualization</guid>
	<pubDate>Wed, 21 Mar 2018 12:25:20 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36012/gmol-an-interactive-tool-for-3d-genome-structure-visualization</link>
	<title><![CDATA[GMOL: An Interactive Tool for 3D Genome Structure Visualization]]></title>
	<description><![CDATA[<p><span>GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.</span></p><p>Address of the bookmark: <a href="https://www.nature.com/articles/srep20802" rel="nofollow">https://www.nature.com/articles/srep20802</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18580/faculty-positions-at-central-university-of-punjab-bathinda</guid>
  <pubDate>Wed, 22 Oct 2014 10:45:37 -0500</pubDate>
  <link></link>
  <title><![CDATA[Faculty Positions at CENTRAL UNIVERSITY OF PUNJAB, BATHINDA]]></title>
  <description><![CDATA[
<p>Advertisement No. T/NT-01 (2014)</p>

<p>Faculty Positions<br />The Central University of Punjab (CUP), Bathinda will be having the Schools and Departments as given in Table-I. The University invites applications from eligible candidates for the posts of Professors (Pay Band Rs. 37400-67000 with AGP of Rs. 10, 000/-), Associate Professors (Pay Band Rs.37400-67000 with AGP of Rs. 9,000/-) and Assistant Professors (Pay Band Rs.15600-39100 with AGP of Rs. 6,000/-)</p>

<p>POSITION AVAILABLE IN THE AREA OF SPECIALIZTION</p>

<p>3. Bioinformatics,</p>

<p>Procedure to apply: Application forms along with API form complete in all respect along with necessary documents and application fee of Rs. 750/-. (Rs. 250/- for Scheduled Caste/Scheduled Tribe/Person with disabilities) should be sent to:</p>

<p>Registrar (Officiating)<br />Central University of Punjab<br />City Campus, Mansa Road<br />Bathinda-151 001</p>

<p>Application forms from the prospective candidates are accepted upto November 10, 2014.</p>

<p>Based on the qualification of the candidates and the need of the university, the applications received will be processed through appropriately constituted selection committees shortly. Minimum qualification can be relaxed in case of exceptionally outstanding candidate. For further details visit www.cup.ac.in; www.centralunipunjab.com; www.cup.edu.in</p>

<p>The candidate should download the application form available at website www.cup.ac.in;<br />www.centralunipunjab.com; and submit it complete in all respects on or before 10th November 2014.</p>

<p>Those who have applied earlier need to submit Academic Performance Index (API) form, 5 copies of Summary of the Application Form (available at: www.cup.ac.in; www.centralunipunjab.com and Updated CV if not updated recently (without application fee).</p>

<p>http://cup.edu.in/Faculty_details_and_general_instructions.pdf</p>

<p>http://cup.edu.in/Final%20Application%20and%20summary%20Sheet%20and%20Api%20form.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41736/synvisio-an-interactive-multiscale-synteny-visualization-tool-for-mcscanx</guid>
	<pubDate>Sun, 31 May 2020 02:01:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41736/synvisio-an-interactive-multiscale-synteny-visualization-tool-for-mcscanx</link>
	<title><![CDATA[SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.]]></title>
	<description><![CDATA[<p>SynVisio lets you explore the results of&nbsp;<a href="http://chibba.pgml.uga.edu/mcscan2/">McScanX</a>&nbsp;a popular synteny and collinearity detection toolkit and generate publication ready images.</p>
<p>SynVisio requires two files to run:</p>
<ul>
<li>The&nbsp;<strong>simplified gff file</strong>&nbsp;that was used as an input for a McScanX query.</li>
<li>The&nbsp;<strong>collinearity file</strong>&nbsp;generated as an output by McScanX for the same input query.</li>
<li>Optional&nbsp;<strong>track file</strong>&nbsp;in bedgraph format to annotate the generated charts.</li>
</ul>
<p>SynVisio offers different types of visualizations such as&nbsp;<strong>Linear Parallel plots</strong>,&nbsp;<strong>Hive plots</strong>,&nbsp;<strong>Stacked Parallel Plots&nbsp;</strong>and&nbsp;<strong>Dot plots</strong>. Users can configure the type of plots required and then choose the source and the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.</p><p>Address of the bookmark: <a href="https://synvisio.github.io/#/" rel="nofollow">https://synvisio.github.io/#/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19020/jrf-in-bioinformatics-bioinformatics-centre-north-eastern-hill-university</guid>
  <pubDate>Thu, 06 Nov 2014 10:24:05 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF in Bioinformatics @ Bioinformatics Centre, North-Eastern Hill University]]></title>
  <description><![CDATA[
<p>Applications with complete bio-data are invited for JRF (3) and Project Assistant (1) in a DBT project "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India" sanctioned for a period of 3 years.</p>

<p>Details are available at www.nehu.ac.in and www.bicnehu.ac.in.</p>

<p>Applications must reach the undersigned within 15 days from the date of publication of this advertisement.</p>

<p>Prof. Pramod Tandon. PI/Mr. Devendra Kumar Biswal (Co-PI)</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome</guid>
	<pubDate>Thu, 08 Aug 2024 23:31:18 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome</link>
	<title><![CDATA[Tools to access the quality of your assembled genome !]]></title>
	<description><![CDATA[<ul dir="auto">
<li><a href="https://github.com/linsalrob/fasta_validator">FASTA VALIDATOR</a>&nbsp;+&nbsp;<a href="https://github.com/shenwei356/seqkit">SEQKIT RMDUP</a>: FASTA validation</li>
<li><a href="https://genometools.org/tools/gt_gff3validator.html">GENOMETOOLS GT GFF3VALIDATOR</a>: GFF3 validation</li>
<li><a href="https://github.com/PlantandFoodResearch/assemblathon2-analysis/blob/a93cba25d847434f7eadc04e63b58c567c46a56d/assemblathon_stats.pl">ASSEMBLATHON STATS</a>: Assembly statistics</li>
<li><a href="https://genometools.org/tools/gt_stat.html">GENOMETOOLS GT STAT</a>: Annotation statistics</li>
<li><a href="https://github.com/ncbi/fcs">NCBI FCS ADAPTOR</a>: Adaptor contamination pass/fail</li>
<li><a href="https://github.com/ncbi/fcs">NCBI FCS GX</a>: Foreign organism contamination pass/fail</li>
<li><a href="https://gitlab.com/ezlab/busco">BUSCO</a>: Gene-space completeness estimation</li>
<li><a href="https://github.com/tolkit/telomeric-identifier">TIDK</a>: Telomere repeat identification</li>
<li><a href="https://github.com/oushujun/LTR_retriever/blob/master/LAI">LAI</a>: Continuity of repetitive sequences</li>
<li><a href="https://github.com/DerrickWood/kraken2">KRAKEN2</a>: Taxonomy classification</li>
<li><a href="https://github.com/igvteam/juicebox.js">HIC CONTACT MAP</a>: Alignment and visualisation of HiC data</li>
<li><a href="https://github.com/mummer4/mummer">MUMMER</a>&nbsp;&rarr;&nbsp;<a href="http://circos.ca/documentation/">CIRCOS</a>&nbsp;+&nbsp;<a href="https://plotly.com/">DOTPLOT</a>&nbsp;&amp;&nbsp;<a href="https://github.com/lh3/minimap2">MINIMAP2</a>&nbsp;&rarr;&nbsp;<a href="https://github.com/schneebergerlab/plotsr">PLOTSR</a>: Synteny analysis</li>
<li><a href="https://github.com/marbl/merqury">MERQURY</a>: K-mer completeness, consensus quality and phasing assessment</li>
</ul>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42303/fqc-dashboard-integrates-fastqc-results-into-a-web-based-interactive-and-extensible-fastq-quality-control-tool</guid>
	<pubDate>Tue, 10 Nov 2020 01:30:22 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42303/fqc-dashboard-integrates-fastqc-results-into-a-web-based-interactive-and-extensible-fastq-quality-control-tool</link>
	<title><![CDATA[FQC Dashboard: Integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool]]></title>
	<description><![CDATA[<p>FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The dashboard groups samples in dropdowns for navigation among the data sets, utilizes human-readable configuration files to manipulate the pages and tabs, and is extensible with CSV data.</p><p>Address of the bookmark: <a href="https://github.com/pnnl/fqc" rel="nofollow">https://github.com/pnnl/fqc</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19162/icgeb-bioinformatics-rasrfjrf-vacancies</guid>
  <pubDate>Thu, 13 Nov 2014 13:39:30 -0600</pubDate>
  <link></link>
  <title><![CDATA[ICGEB Bioinformatics RA/SRF/JRF Vacancies]]></title>
  <description><![CDATA[
<p>Research Associate/JRF/SRF position, DBT Sponsored Bioinformatics Infrastructure Facility</p>

<p>Applicants should hold a PhD or a first class MSc/MTech degree in Bioinformatics of Biotechnology/Life Sciences; experience in using bioinformatics tools, working in Linux and knowledge of computer network administration.</p>

<p>Submit CV and letter of interest by email to: Dr. Dinesh Gupta atdinesh@icgeb.res.in</p>
]]></description>
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