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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/14191?offset=990</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39624/cogent-a-tool-for-reconstructing-the-coding-genome-using-high-quality-full-length-transcriptome-sequences</guid>
	<pubDate>Tue, 18 Jun 2019 05:33:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39624/cogent-a-tool-for-reconstructing-the-coding-genome-using-high-quality-full-length-transcriptome-sequences</link>
	<title><![CDATA[Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.]]></title>
	<description><![CDATA[<div id="yui_3_14_1_1_1560853173251_3865">Cogent is a tool that identifies gene&nbsp;families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check&nbsp;assemblies&nbsp;for the presence of&nbsp;these known coding sequences.</div>
<div>&nbsp;</div>
<div>
<p>Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on&nbsp;<a href="https://github.com/PacificBiosciences/cDNA_primer/wiki">Iso-Seq data</a>&nbsp;and in cases where there is no reference genome or the ref genome is highly incomplete.</p>
<p>See a&nbsp;<a href="https://www.dropbox.com/s/mn6hwhguh0pqceu/20160106_Cogent_developers_conference_slides_Cuttlefish.pdf?dl=0">recent presentation</a>&nbsp;on Cogent being applied to the Cuttlefish Iso-Seq data.</p>
<p><a href="https://www.dropbox.com/s/kz0gi7qg0w82k9a/20161026_Cogent_manuscript_forGitHub.pdf?dl=0">Cogent preliminary draft paper (updated 2016Dec version)</a>,&nbsp;<a href="https://www.dropbox.com/s/37412o8glvnfhf9/20161026_Cogent_ManuscriptPlusSupplement_forGitHub.pdf?dl=0">Supplementary</a></p>
<p>Please see&nbsp;<a href="https://github.com/Magdoll/Cogent/wiki">wiki</a>&nbsp;for details on usage.</p>
</div><p>Address of the bookmark: <a href="https://github.com/Magdoll/Cogent" rel="nofollow">https://github.com/Magdoll/Cogent</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/16160/research-scientist-%E2%80%93-bioinformatics-at-sidra-medical-and-research-center</guid>
  <pubDate>Wed, 10 Sep 2014 14:35:35 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Scientist – Bioinformatics at Sidra Medical and Research Center]]></title>
  <description><![CDATA[
<p>Sidra Medical and Research Center(Doha, Qatar) is looking for talented Research Scientists (Bioinformatics / NGS Data Analysis).</p>

<p>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.</p>

<p>Please check the details of the opening and apply here: http://careers.sidra.org/sidra/Vacan...acancyID=60181</p>
]]></description>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/16472/internship-nipgr</guid>
  <pubDate>Sat, 13 Sep 2014 16:02:35 -0500</pubDate>
  <link></link>
  <title><![CDATA[INTERNSHIP @ NIPGR]]></title>
  <description><![CDATA[
<p>Applications are invited from suitable candidates for six months ‘Training Fellowship' at National Institute of Plant Genome Research (NIPGR).</p>

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

<p>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.</p>

<p>About the Internship:</p>

<p>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.</p>

<p>Who can apply:</p>

<p>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.</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41669/filtlong-quality-filtering-tool-for-long-reads</guid>
	<pubDate>Wed, 13 May 2020 10:23:55 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41669/filtlong-quality-filtering-tool-for-long-reads</link>
	<title><![CDATA[Filtlong: quality filtering tool for long reads]]></title>
	<description><![CDATA[<p>Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.</p>
<p>Filtlong builds into a stand-alone executable:</p>
<pre><code>git clone https://github.com/rrwick/Filtlong.git
cd Filtlong
make -j
bin/filtlong -h
</code></pre><p>Address of the bookmark: <a href="https://github.com/rrwick/Filtlong" rel="nofollow">https://github.com/rrwick/Filtlong</a></p>]]></description>
	<dc:creator>Radha Agarkar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/16682/java-utilities-for-next-generation-sequencing-by-pierre-lindenbaum</guid>
	<pubDate>Mon, 15 Sep 2014 17:24:49 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/16682/java-utilities-for-next-generation-sequencing-by-pierre-lindenbaum</link>
	<title><![CDATA[Java utilities for Next Generation Sequencing  by Pierre Lindenbaum]]></title>
	<description><![CDATA[<div>
<div>
<p>Java utilities for Bioinformatics</p>
</div>
<div>
<p><a href="https://github.com/lindenb/jvarkit">https://github.com/lindenb/jvarkit</a></p>
</div>
</div><p>Address of the bookmark: <a href="https://github.com/lindenb/jvarkit" rel="nofollow">https://github.com/lindenb/jvarkit</a></p>]]></description>
	<dc:creator>Robert M Willioms</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41916/truvari-structural-variant-comparison-tool-for-vcfs</guid>
	<pubDate>Tue, 30 Jun 2020 21:30:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41916/truvari-structural-variant-comparison-tool-for-vcfs</link>
	<title><![CDATA[truvari: Structural variant comparison tool for VCFs]]></title>
	<description><![CDATA[<p>Structural variant comparison tool for VCFs</p>
<p>Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure.</p>
<p><a href="https://github.com/spiralgenetics/www.spiralgenetics.com">Spiral Genetics</a></p>
<p><a href="https://docs.google.com/presentation/d/17mvC1XOpOm7khAbZwF3SgtG2Rl4M9Mro37yF2nN7GhE/edit">Motivation</a></p><p>Address of the bookmark: <a href="https://github.com/spiralgenetics/truvari" rel="nofollow">https://github.com/spiralgenetics/truvari</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/17505/kau-thrissur-biotechbioinformatics-rasrfjrftraineestudentships</guid>
  <pubDate>Fri, 26 Sep 2014 20:07:28 -0500</pubDate>
  <link></link>
  <title><![CDATA[KAU Thrissur Biotech/Bioinformatics RA/SRF/JRF/Trainee/Studentships]]></title>
  <description><![CDATA[
<p>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.</p>

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

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

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

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

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

<p>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 &amp; 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”.</p>

<p>*Emoluments are likely to be revised in 2014-2015</p>

<p>More at http://www.kaubic.in/downloads/Notification_bic.pdf<br />http://www.kaubic.in/downloads/Application%20form.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42155/clustergrammer-is-a-web-based-tool-for-visualizing-high-dimensional-data-as-an-interactive-and-shareable-hierarchically-clustered-heatmap</guid>
	<pubDate>Sun, 23 Aug 2020 19:30:17 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42155/clustergrammer-is-a-web-based-tool-for-visualizing-high-dimensional-data-as-an-interactive-and-shareable-hierarchically-clustered-heatmap</link>
	<title><![CDATA[Clustergrammer is a web-based tool for visualizing high-dimensional data as an interactive and shareable hierarchically clustered heatmap]]></title>
	<description><![CDATA[<p><span>Clustergrammer is a web-based tool for visualizing high-dimensional data (e.g. a matrix) as an interactive and shareable hierarchically clustered heatmap. Clustergrammer's front end (</span><a href="http://clustergrammer.readthedocs.io/clustergrammer_js.html#clustergrammer-js">Clustergrammer-JS</a><span>) is built using&nbsp;</span><a href="https://d3js.org/">D3.js</a><span>&nbsp;and its back-end (</span><a href="http://clustergrammer.readthedocs.io/clustergrammer_py.html#clustergrammer-py">Clustergrammer-PY</a><span>) is built using Python. Clustergrammer produces highly interactive visualizations that enable intuitive exploration of high-dimensional data and has several biology-specific features (e.g. enrichment analysis, see&nbsp;</span><a href="http://clustergrammer.readthedocs.io/biology_specific_features.html#biology-specific-features">Biology-Specific Features</a><span>) to facilitate the exploration of gene-level biological data.&nbsp;</span></p><p>Address of the bookmark: <a href="https://github.com/MaayanLab/clustergrammer" rel="nofollow">https://github.com/MaayanLab/clustergrammer</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/17894/faculty-position-at-national-institute-of-technology-rourkela</guid>
  <pubDate>Sun, 05 Oct 2014 15:45:13 -0500</pubDate>
  <link></link>
  <title><![CDATA[FACULTY POSITION at NATIONAL INSTITUTE OF TECHNOLOGY, ROURKELA]]></title>
  <description><![CDATA[
<p>NIT, Rourkela, an institute of national importance under Ministry of HRD, Govt. of India invites applications from Indian nationals possessing excellent academic background along with commitment to quality teaching and research for faculty positions at the level of Professor, Associate Professor and Assistant Professor in most branches of Engineering, Science, Management and Humanities as per following table:-</p>

<p>    1 Asst. Professor (on Pre-Ph.D. Contract)</p>

<p>    2 Asst. Professor (on Contract)</p>

<p>    3 Asst. Professor</p>

<p>    4 Associate Professor</p>

<p>    5 Professor</p>

<p>Life Sciences:-</p>

<p>    i)Biochemistry and Molecular Biology; ii)Cell and Developmental Biology; iii)Immunology and Molecular Medicine; (iv) Microbiology and Ecology (v)Bioinformatics Group; vi)Biophysical Sciences</p>

<p>HOW TO APPLY:-</p>

<p>a. Candidates willing to apply for one or more posts are requested to apply online at “http://www.nitrkl.ac.in/ JOBS &amp; TENDERS /Faculty Position” .<br />b. Persons employed in Government and Semi-Government organizations may apply directly against the standing advertisement. For this the application should be completed online. The printout of the application generated online should be submitted through employer if shortlisted for interview.<br />c. The online application can be filled in multiple sessions.<br />d. Candidates are required to check the Institute website from time to time for latest information, application status call for interview, change of dates and final results.<br />e. Applications shall be received online only. Please do not send application or CV against this advertisement by email or letter mail.</p>

<p>More Info: http://nitrkl.ac.in/Jobs_Tenders/1FacultyPosition/Default.aspx</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43090/loretta-a-user-friendly-tool-for-assembling-viral-genomes-from-pacbio-sequence-data</guid>
	<pubDate>Wed, 23 Jun 2021 07:54:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43090/loretta-a-user-friendly-tool-for-assembling-viral-genomes-from-pacbio-sequence-data</link>
	<title><![CDATA[LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data]]></title>
	<description><![CDATA[<p>LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing <em>de novo</em> assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads.</p>
<p>https://academic.oup.com/ve/article/7/1/veab042/6248116</p><p>Address of the bookmark: <a href="https://academic.oup.com/ve/article/7/1/veab042/6248116" rel="nofollow">https://academic.oup.com/ve/article/7/1/veab042/6248116</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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