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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44716?offset=960</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly</guid>
	<pubDate>Tue, 17 Aug 2021 13:17:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly</link>
	<title><![CDATA[Bioinformatics tools for telomere to telomere assembly !]]></title>
	<description><![CDATA[<p>●&nbsp;<a href="https://github.com/arangrhie/merfin" target="_blank">Merfin</a>&nbsp;&ndash; k-mer-based assembly and variant calling evaluation for improved consensus accuracy (Arang Rhie)<br />●&nbsp;<a href="https://www.biorxiv.org/content/10.1101/2020.11.11.378133v1" target="_blank">PanGenie</a>&nbsp;&ndash; algorithm that leverages a pangenome reference built from haplotype-resolved genome assemblies in conjunction with k-mer count information from raw, short-read sequencing data to genotype a wide spectrum of genetic variation (Tobias Marschall)<br />●&nbsp;<a href="https://github.com/ConesaLab/SQANTI3" target="_blank">SQANTI3</a>&nbsp;&ndash; an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline (Roc&iacute;o Amor&iacute;n de Heged&uuml;s&nbsp;<a href="https://twitter.com/rocioadh" target="_blank">@rocioadh</a>)<br />●&nbsp;<a href="https://github.com/GenomeRIK/tama" target="_blank">tama</a>&nbsp;(Transcriptome Annotation by Modular Algorithms) &ndash; software designed for processing Iso-Seq data and other long-read transcriptome data (Richard Kuo&nbsp;<a href="https://twitter.com/GenomeRIK" target="_blank">@GenomeRIK</a>)<br />●&nbsp;<a href="https://github.com/PacificBiosciences/pbAA" target="_blank">pbaa</a>&nbsp;(PacBio Amplicon Analysis) &ndash; separates complex mixtures of amplicon targets from genomic samples to cluster and generate high-quality consensus sequences from HiFi reads (Zev Kronenberg&nbsp;<a href="https://twitter.com/zevkronenberg" target="_blank">@zevkronenberg</a>)<br />●&nbsp;<a href="https://github.com/yuanyuan929/bellerophon" target="_blank">bellerophon</a>&nbsp;&ndash; analyzes MHC typing and other low-complexity gene amplicon data; performs allele calling while detecting polymorphic sites within the sequences and removing potential chimeric sequence variants (Yuanyuan Cheng&nbsp;<a href="https://twitter.com/Yuanyuan929" target="_blank">@Yuanyuan929</a>)<br />●&nbsp;<a href="https://github.com/amwenger/svpack" target="_blank">svpack</a>&nbsp;&ndash; tools for filtering, comparing, and annotating structural variant (SV) calls in VCF format (Aaron Wenger)<br />●&nbsp;<a href="https://github.com/AntonBankevich/jumboDB" target="_blank">JumboDB</a>&nbsp;&ndash; tool for de Bruijn graph construction (Anton Bankevich&nbsp;<a href="https://twitter.com/AntonBankevich" target="_blank">@AntonBankevich</a>)<br />●&nbsp;<a href="https://github.com/ksahlin/ultra" target="_blank">uLTRA</a>&nbsp;&ndash; tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations. (Kristoffer Sahlin&nbsp;<a href="https://twitter.com/krsahlin" target="_blank">@krsahlin</a>)<br />●&nbsp;<a href="https://www.biorxiv.org/content/10.1101/2021.01.25.428044v1.full.pdf" target="_blank">LeafGo</a>&nbsp;&ndash; workflow to rapidly produce high-quality de novo plant genomes (Luca Ermini&nbsp;<a href="https://twitter.com/ermini_luca" target="_blank">@ermini_luca</a>)</p><p>Reference:</p><p>https://www.pacb.com/blog/young-investigators-share-stellar-science-career-advice-and-bioinformatics-tools-at-smrt-leiden-2021/</p><p>&nbsp;</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics</guid>
	<pubDate>Thu, 18 Dec 2014 11:05:42 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics</link>
	<title><![CDATA[Google Genomics]]></title>
	<description><![CDATA[<ul>
<li>
<p><strong>Explore genetic variation interactively.</strong> Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.</p>
</li>
<li>
<p><strong>Process big genomic data easily.</strong> Run batch analyses like principal component analysis and Hardy-Weinberg equilibrium on as many samples as you like, in minutes or hours, with just a little code.</p>
</li>
<li>
<p><strong>Use Google's infrastructure and big data expertise.</strong> Store one genome or a million using Google Genomics and take advantage of the same infrastructure that powers Search, Maps, YouTube, Gmail and Drive.</p>
</li>
<li>
<p><strong>Support emerging global standards.</strong> Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.</p>
</li>
</ul><p>Address of the bookmark: <a href="https://cloud.google.com/genomics/" rel="nofollow">https://cloud.google.com/genomics/</a></p>]]></description>
	<dc:creator>Tenzin Paul</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44288/upset-plots</guid>
	<pubDate>Fri, 24 Mar 2023 22:30:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44288/upset-plots</link>
	<title><![CDATA[Upset plots !]]></title>
	<description><![CDATA[<p>Upset plots are a type of visualization used to analyze the intersection of sets or categories. They are particularly useful for displaying data with multiple categories and analyzing their overlaps.</p>
<p>In an upset plot, each row represents a category or set, and each column represents a data point. The length of the bar for each category indicates the number of data points that belong to that category. The plot also shows the intersections between categories, represented by overlapping bars.</p>
<p>Upset plots are useful for visualizing complex data with multiple categories and intersections, and can help identify patterns and relationships between categories. They are often used in fields such as bioinformatics, where they can be used to analyze gene expression data or to compare the results of different experimental conditions.</p>
<p>https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions</p><p>Address of the bookmark: <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions" rel="nofollow">https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19600/studentship-at-nagaland-university</guid>
  <pubDate>Tue, 16 Dec 2014 01:35:00 -0600</pubDate>
  <link></link>
  <title><![CDATA[Studentship at Nagaland University]]></title>
  <description><![CDATA[
<p>Nagaland University<br />(A Central University Estd. By the Act of Parliament No. 35 of 1989)<br />Lumami 798 627, Nagaland<br />DBT Sponsored ‘Bioinformatics Infrastructure Facility’ Centre</p>

<p>Applications in plain paper are invited for the posts of (1) Traineeship (2 Nos.) and (2) Studentship – (2 Nos.) in the DBT funded-Bioinformatics Infrastructure Facility (BIF), Nagaland University, Lumami-798627, Nagaland. Details are given below. Interested candidates may submit the application along with self attested copies of certificates in support of the candidature to Prof. Chitta Ranjan Deb, Coordinator or Dr. L. N. Kakati, Deputy Coordinator, BIF Centre, Nagaland University, Lumami-798627, Nagaland on or before 15th January 2015.</p>

<p>The scanned application with relevant documents may be sent by email attachment to bifnulumami@gmail.com. Shortlisted candidates will be informed by email if called for interview. No TA/DA is admissible for attending the interview.</p>

<p>Traineeship (Two nos.)</p>

<p>    Post Graduate degree in any branch of Life Sciences from UGC recognized Universities</p>

<p>    Knowledge of computers and bioinformatics</p>

<p>    Rs.8000/- p.m. fixed.</p>

<p>    6 months</p>

<p>Studentship (Two nos.)</p>

<p>    Pursuing Post Graduate degree in any branch of Life Sciences from UGC recognized Universities</p>

<p>    Knowledge of computers and bioinformatics</p>

<p>    Rs.8000/- p.m. fixed.</p>

<p>    6 months</p>

<p>Terms and Conditions:</p>

<p>i) Applicants need to produce all original documents if call for interview.<br />ii) The posts are purely temporary and the appointment does not confer any entitlement or right over the job and will not be considered as formal service.<br />iii) No TA &amp; DA will be paid for appearing in the walk-in-interview.<br />iv) The stipend/salary amount is subject to the sanction of DBT, New Delhi.</p>

<p>Advertisement: http://www.nagauniv.org.in/files/BIF%20Advt.pdf</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19729/senior-scientist-agricultural-bio-informatics-one-post</guid>
  <pubDate>Wed, 24 Dec 2014 05:01:02 -0600</pubDate>
  <link></link>
  <title><![CDATA[Senior Scientist (Agricultural Bio-informatics) (One post)]]></title>
  <description><![CDATA[
<p>Agricultural Scientists Recruitment Board</p>

<p>Qualifications Essential:<br />Doctoral degree in Bio-informatics/ Biotechnology/Molecular Biology and Biotechnology/Life Sciences/ Computer Sciences with specialization in Bio-informatics including relevant basic sciences with 8 years’ experience in the relevant subject as Scientist/Lecturer or in an equivalent position in the Pay Band- 3 of 15600-39100 with Grade Pay of 5400/6000/7000/8000 having made contribution to research/teachin/extension education as evidenced by published work/innovations and impact. </p>

<p>OR </p>

<p>Doctoral degree in the above subject(s) including relevant basic sciences with minimum 8 years’ experience of high quality post-doctoral research in an institution/organization as evidenced by at least 6 publications in journals with NAAS rating of 7.5 or above.</p>

<p>Desirable:<br />(i) Specialization and experience: Knowledge of software development and its application in crop bioinformatics, experience in handling ‘omies’data. <br />(ii) Teaching experience in relevant subject</p>

<p>The Secretary, Agricultural Scientists Recruitment Board, Indian Council of Agricultural Research Krishi Anusandhan Bhavan-I, Pusa New Delhi –110 012, India</p>

<p>Detailed eligibility criteria with how to apply information can be had at:<br />http://www.indiastudychannel.com/jobs/333467-Indian-Council-of-Agricultural-Research-looking-for-Assistant-Director-General.aspx</p>

<p>More at http://asrb.org.in/administrator/uploads_dir/1418978057english.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/19820/rstudio</guid>
	<pubDate>Sat, 27 Dec 2014 06:50:58 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/19820/rstudio</link>
	<title><![CDATA[RStudio]]></title>
	<description><![CDATA[<p>RStudio IDE is a powerful and productive user interface for R. It&rsquo;s free and open source, and works great on Windows, Mac, and Linux.</p>
<p>The developers and expert trainers are the authors of several popular R packages, including ggplot2, plyr, lubridate, and others.</p>
<p>More at http://www.rstudio.com/</p>
<p>http://www.rstudio.com/products/RStudio/</p><p>Address of the bookmark: <a href="http://www.rstudio.com/" rel="nofollow">http://www.rstudio.com/</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/19980/seqloc-06</guid>
	<pubDate>Sun, 28 Dec 2014 12:51:29 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/19980/seqloc-06</link>
	<title><![CDATA[seqloc 0.6]]></title>
	<description><![CDATA[<p>The <code>Bio.SeqLoc</code> modules in <code>seqloc</code> are designed to represent positions and locations (ranges of positions) on sequences, particularly nucleotide sequences. My original motivation for writing these packages was handing the locations of genes in eukaryotic genomes.</p>
<p>Handle sequence locations for bioinformatics http://www.ingolia-lab.org/seqloc-tutorial.html</p><p>Address of the bookmark: <a href="http://www.stackage.org/snapshot/nightly-2014-12-28/package/seqloc-0.6" rel="nofollow">http://www.stackage.org/snapshot/nightly-2014-12-28/package/seqloc-0.6</a></p>]]></description>
	<dc:creator>Gudiya Pal</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/20271/research-associate-tata-memorial-centre-advanced-centre-for-treatment-research-and-education-in-cancer-kharghar-navi-mumbai</guid>
  <pubDate>Thu, 08 Jan 2015 20:53:57 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Associate	@ TATA MEMORIAL CENTRE ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER KHARGHAR, NAVI MUMBAI]]></title>
  <description><![CDATA[
<p>TATA MEMORIAL CENTRE ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER KHARGHAR, NAVI MUMBAI – 410210</p>

<p>Website: www.actrec.gov.in; Ph: 27405000</p>

<p>No. ACTREC/Advt./ 66 /2014 23rd December, 2014<br />Research Associate	</p>

<p>International Cancer Genome Consortium (ICGC) - India Project (IRB Project No. 3 A/c. No. 2408)</p>

<p>Dr. Rajiv Sarin</p>

<p>Duration of the Project: One year Extendable up to Three years.</p>

<p>Consolidated Salary: Rs. 42,000/- p.m.</p>

<p>Application last date: 8th January, 2015.</p>

<p>Interview Date &amp; Time: 21st January, 2015, at 11.00 a.m.</p>

<p>Venue: Conference Room, 3rd floor, Khanolkar Shodhika, ACTREC.</p>

<p>Essential Qualifications and Experience:</p>

<p>Ph.D (any branch of Life Sciences)</p>

<p>The candidate must have at least one year experience after Ph.D., preferably in Genomics and Molecular Biology.</p>

<p>Candidates fulfilling these requirements should pre register themselves by sending their application in the prescribed format with recent CV and contact details of 2 referees by e-mail to icgc@actrec.gov.in latest 8th January, 2015 by 10.00 a.m.</p>

<p>Candidates shortlisted for the interview will be intimated by email on or before 9th January, 2015.</p>

<p>The interviews would be held on 21st January 2015 and will be only for the pre registered candidates who have been shortlisted.<br />No T.A./D.A. will be admissible for attending the interview.</p>

<p>At the time of Interview the candidate should bring original certificates along with CV with contact details of 2 referees and submit the photocopies (attested) of the certificates, with a recent passport size photograph.</p>

<p>Advertisement: www.actrec.gov.in/data%20files/2014/Walk-in-Research-Fellow-26-12-14.doc</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/20454/comparative-genomics-in-ensembl</guid>
	<pubDate>Wed, 21 Jan 2015 08:31:11 -0600</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/20454/comparative-genomics-in-ensembl</link>
	<title><![CDATA[Comparative Genomics in Ensembl]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/dDRdCnZOMCM" frameborder="0" allowfullscreen></iframe>The Ensembl browser provides viewable whole-genome alignments, homologues and phylogenetic gene trees, protein families, and ancestral sequences.  Learn how to view and export these data in this video.]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/20471/bioinformatics-scripts</guid>
	<pubDate>Thu, 22 Jan 2015 22:29:39 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/20471/bioinformatics-scripts</link>
	<title><![CDATA[Bioinformatics Scripts]]></title>
	<description><![CDATA[<p>Some of the useful bioinformatics scripts.</p>
<p>For example ... contig-stats.pl is a Perl script that will automatically describe features of a sequence assembly.</p>
<p>http://milkweedgenome.org/?q=scripts</p><p>Address of the bookmark: <a href="http://milkweedgenome.org/?q=scripts" rel="nofollow">http://milkweedgenome.org/?q=scripts</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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