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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30074?offset=510</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36884/halc-high-throughput-algorithm-for-long-read-error-correction</guid>
	<pubDate>Fri, 08 Jun 2018 10:47:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36884/halc-high-throughput-algorithm-for-long-read-error-correction</link>
	<title><![CDATA[HALC: High throughput algorithm for long read error correction]]></title>
	<description><![CDATA[HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig region, including its true genome region’s repeats in the contigs sufficiently similar to it (similar repeat based alignment approach)

HALC was able to obtain 6.7-41.1% higher throughput than the existing algorithms while maintaining comparable accuracy. The HALC corrected long reads can thus result in 11.4-60.7% longer assembled contigs than the existing algorithms.<p>Address of the bookmark: <a href="https://github.com/lanl001/halc" rel="nofollow">https://github.com/lanl001/halc</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/11592/xampp-starting-apache-fail-ubuntu</guid>
	<pubDate>Sat, 07 Jun 2014 05:52:35 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/11592/xampp-starting-apache-fail-ubuntu</link>
	<title><![CDATA[XAMPP: Starting Apache fail Ubuntu]]></title>
	<description><![CDATA[<p>Once you install XAMMP on linux, the most common problem you face is Apache failure. To fix the issues please use following command to first stop and then again start it.</p><p>sudo /etc/init.d/apache2 stop</p><p>sudo /etc/init.d/mysql stop</p><p>sudo /etc/init.d/proftpd stop</p><p>sudo /opt/lampp/lampp start</p><p>&nbsp;</p><p><strong>PhpMyAdmin &ldquo;Wrong permissions on configuration file, should not be world writable!&rdquo;</strong></p><p>Once the Xammp is installed, it might be possible to set up the configuration file in writable mode. Try the following steps:</p><p>Just chmod 0755 the file</p><pre>sudo chmod 0755 config.inc.php</pre>]]></description>
	<dc:creator>Ram Yash Pal</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37502/alignqc-a-tool-for-assessing-an-alignment-and-generating-reports-that-are-easy-to-share</guid>
	<pubDate>Tue, 07 Aug 2018 04:41:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37502/alignqc-a-tool-for-assessing-an-alignment-and-generating-reports-that-are-easy-to-share</link>
	<title><![CDATA[AlignQC: A tool for assessing an alignment, and generating reports that are easy to share]]></title>
	<description><![CDATA[<p><span>Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.</span></p>
<p>https://f1000research.com/articles/6-100/</p>
<p>https://github.com/jason-weirather/AlignQC</p><p>Address of the bookmark: <a href="https://www.healthcare.uiowa.edu/labs/au/AlignQC/" rel="nofollow">https://www.healthcare.uiowa.edu/labs/au/AlignQC/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37993/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data</guid>
	<pubDate>Thu, 25 Oct 2018 06:14:55 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37993/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data</link>
	<title><![CDATA[Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data]]></title>
	<description><![CDATA[<p><strong>Platypus</strong><span>&nbsp;is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on&nbsp;</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=24463883">whole-genome</a><span>,&nbsp;</span><a href="http://www.nature.com/ng/journal/v45/n1/abs/ng.2492.html">exon-capture</a><span>, and&nbsp;</span><a href="http://www.nature.com/nature/journal/v493/n7432/abs/nature11725.html">targeted capture</a><span>&nbsp;data, it has been run on very large datasets as part of the&nbsp;</span><a href="http://www.1000genomes.org/">Thousand Genomes</a><span>&nbsp;and WGS500 projects, and is being used in clinical sequencing trials in the&nbsp;</span><a href="http://www.mcgprogramme.com/">Mainstreaming Cancer Genetics</a><span>&nbsp;programme.&nbsp;</span></p>
<p><span>Tutorial&nbsp;https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt</span></p><p>Address of the bookmark: <a href="http://www.well.ox.ac.uk/platypus" rel="nofollow">http://www.well.ox.ac.uk/platypus</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/12594/faculty-positions-at-central-university-of-punjab</guid>
  <pubDate>Mon, 07 Jul 2014 23:33:33 -0500</pubDate>
  <link></link>
  <title><![CDATA[Faculty Positions at Central University of Punjab]]></title>
  <description><![CDATA[
<p>Faculty Positions: Rolling/Open Advertisement Advt.No: T-10 (2013)</p>

<p>Pay Scale: Pay Band Rs.15600-39100 with AGP of Rs.6,000/-</p>

<p>Essential Qualifications for Professors, Associate Professors, and Assistant Professors: As per “UGC REGULATIONS ON MINIMUM QUALIFICATIONS FOR APPOINTMENT OF TEACHERS AND OTHER ACADEMIC STAFF IN UNIVERSITIES AND COLLEGES AND MEASURES FOR THE MAINTENANCE OF STANDARDS IN HIGHER EDUCATION 2010“ and the 2nd Amendments to the regulation issued in June 2013.</p>

<p>For details: http://www.ugc.ac.in/oldpdf/regulations/revised_finalugcregulationfinal10.pdf http://www.ugc.ac.in/pdfnews/8539300_English.pdf and University rules.</p>

<p>Procedure to apply:</p>

<p>Application forms along with API form complete in all respect along with necessary documents and application fee of Rs. 500/-. (Rs. 250/- for Scheduled Caste/Scheduled Tribe/Person with disabilities) should be sent to:</p>

<p>Registrar, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001</p>

<p>For more info visit: http://www.centralunipunjab.com/Teaching/Final%20Details-t10-2013.pdf, http://www.centralunipunjab.com/Teaching/Advertisement-t10-2013.jpg</p>

<p>Last Apply Date: 31 Dec 2014</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39674/simka-and-simkamin-are-comparative-metagenomics-method-dedicated-to-ngs-datasets</guid>
	<pubDate>Sat, 06 Jul 2019 13:56:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39674/simka-and-simkamin-are-comparative-metagenomics-method-dedicated-to-ngs-datasets</link>
	<title><![CDATA[Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets]]></title>
	<description><![CDATA[<p>Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.</p>
<p>Developper:&nbsp;<a href="http://people.rennes.inria.fr/Gaetan.Benoit/">Ga&euml;tan Benoit</a>, PhD, former member of the&nbsp;<a href="http://team.inria.fr/genscale/">Genscale</a>&nbsp;team at Inria.</p>
<p>Contact: claire dot lemaitre at inria dot fr</p>
<p><span>Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets.&nbsp;</span><span></span><span><a href="https://gatb.inria.fr/software/simka/">https://gatb.inria.fr/software/simka/</a></span></p><p>Address of the bookmark: <a href="https://github.com/GATB/simka" rel="nofollow">https://github.com/GATB/simka</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/40770/scientist-bioinformatics-positions</guid>
  <pubDate>Thu, 30 Jan 2020 06:53:40 -0600</pubDate>
  <link></link>
  <title><![CDATA[Scientist Bioinformatics Positions]]></title>
  <description><![CDATA[
<p>Bioinformatics-Multi_Omics_Integration</p>

<p>https://www.researchgate.net/job/939073_Senior_Scientist_Bioinformatics-Multi_Omics_Integration</p>

<p> <br />Senior_Scientist_Bioinformatics-Transcriptomics_Analysis     </p>

<p>https://www.researchgate.net/job/939075_Senior_Scientist_Bioinformatics-Transcriptomics_Analysis-Belgium_France_Switzerland_The_Netherlands</p>

<p>Senior Scientist Bioinformatics - Network Analytics</p>

<p>https://www.researchgate.net/job/939070_Senior_Scientist_Bioinformatics-Network_Analytics_Belgium_France_Switzerland_the_Netherlands</p>

<p>Team Leader Bioinformatics Data Sciences - Mechelen, Belgium</p>

<p>https://www.researchgate.net/job/938787_Team_Leader_Bioinformatics_Data_Sciences-Mechelen_Belgium</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/42329/10-ngs-services-companies-around-the-globe</guid>
	<pubDate>Sun, 22 Nov 2020 23:56:17 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/42329/10-ngs-services-companies-around-the-globe</link>
	<title><![CDATA[10 NGS services companies around the globe !]]></title>
	<description><![CDATA[<p><strong>The global&nbsp;NGS services market&nbsp;is expected to reach USD 13.1 billion by 2025.&nbsp;</strong>Here are the&nbsp;<strong style="font-size: 12.8px;">top 10 NGS services companies to look for &ndash;</strong></p><p><strong>1.&nbsp;<a href="https://www.illumina.com/">Illumina, Inc. (U.S.)</a></strong></p><p>Illumina, Inc. was founded in 1998 and is headquartered at San Diego, U.S. Illumina, Inc. is one of the leading players in DNA sequencing and array-based technologies, serving customers in the research, clinical, and applied markets. The company offers products for applications in the life sciences, oncology, reproductive health, agriculture, and other emerging segments. The company serves government laboratories, genomic research centers, academics institutions as well as pharmaceutical, biotechnology, agrigenomics, commercial molecular diagnostics laboratories and consumer genomics companies. Illumina, Inc. has its geographic presence in North America, Europe, Latin America, Asia-pacific, and others.</p><p><strong>2.&nbsp;<a href="https://www.qiagen.com/us/">QIAGEN N.V. (Netherlands)</a></strong></p><p>QIAGEN N.V. was incorporated in 1986 and is headquartered at Venlo, The Netherlands. The Company is engaged in providing Sample to Insight solutions that transform biological samples into molecular insights. QIAGEN provides its workflow to customers in molecular diagnostics, assay technologies, bioservices and automation systems.&nbsp; The company&rsquo;s genome services are suitable for custom/tailored projects that allow access to genomic sequence information.&nbsp; The Company market its products in more than 100 countries across the Americas, Europe, Asia, Australia, and the Middle-East &amp;Africa through its subsidiaries and channel partners.</p><p><strong>3.&nbsp;<a href="https://www.perkinelmer.com/">PerkinElmer, Inc. (U.S.)</a></strong></p><p>PerkinElmer, Inc. was founded in 1947 and is headquartered in Waltham, Massachusetts, the U.S. PerkinElmer, Inc. offers its products &amp; services and solutions for the diagnostics, food, environmental, industrial, life sciences research and laboratory services markets. The company offer comprehensive genetic testing solutions that help to provide insight into the complex nature of rare and inherited diseases. Some of the subsidiaries of the company are Caliper Life Sciences, Improvision, Viacell Inc., ViaCord LLC, among many others. The company has its facilities located in Europe (France, Germany, and Belgium), U.S. and Asia (China, India, and Japan).</p><p><strong>4.&nbsp;<a href="https://www.eurofins.com/">Eurofins Scientific SE (Luxembourg)</a></strong></p><p>Eurofins Scientific SE was founded in 1987 and is headquartered in Luxembourg, Europe. The company offers a portfolio of over 130,000 analytical methods and more than 150 million assays performed each year to establish the safety, identity, composition, authenticity, origin, traceability, and purity of biological substances and products, as well as carry out human diagnostic services. The company has its geographic presence across 39 countries in Europe, North and South America, and Asia-Pacific.</p><p><strong>5.&nbsp;<a href="https://www.gatc-biotech.com/en/index.html">GATC Biotech AG (Germany)</a></strong></p><p>GATC Biotech AG was founded in 1990 and is headquartered in Constance, Germany. The company provides DNA and RNA sequencing and bioservices solutions to academics and industrial areas. It also provides next generation sequencing services including genomes, targeted (re)-sequencing, human sample sequencing, transcriptomes, metagenomes, regulomes, pre-sequencing, NGS barcode labels, and next generation sequencing technologies; and bioservices services, including bioservices tools, pipelines and workflows, compute resources, data analysis reports, and case studies. GATC Biotech AG operates as a subsidiary of Eurofins Scientific SE. It offers its products through distributors in Italy, Japan, Portugal, Spain, and the Czech Republic.</p><p><strong>6.<a href="https://www.macrogen.com/">&nbsp;Macrogen, Inc. (South Korea)</a></strong></p><p>Macrogen, Inc. was founded in 1997 and is headquartered in Seoul, South Korea. Macrogen, Inc. provides next generation sequencing services such as whole genome, de novo, exome, targeted, transcriptomics, metagenome, and epigenome sequencing.&nbsp; The company also provides a variety of services such as oligo synthesis, database construction, genome research, and bioservices analysis system consulting services. Macrogen, Inc. provides genome research services in Korea and internationally.</p><p><strong>7.&nbsp;<a href="https://www.genotypic.co.in/">Genotypic Technology Pvt. Ltd. (India)</a></strong></p><p>Genotypic Technology Pvt. Ltd. was incorporated in 1998 and is headquartered in Bangalore, India. Genotypic Technology is the first Genomics service provider in India providing Microarray, Next Generation Sequencing (NGS), Bioservices and solutions to domestic/ international pharma, biotech companies and academia. The company provides its services for protocol optimization, probe designing, array layouts, project designing, and nucleic acid analysis to in-depth analysis. Genotypic Technology has its geographic presence in North America, Europe, Asia Pacific, Middle East &amp; Africa, and Latin America.</p><p><strong>8.&nbsp;<a href="https://www.genewiz.com/">GENEWIZ, Inc. (U.S.)</a></strong></p><p>GENEWIZ, Inc. was founded in 1999 and is headquartered in South Plainfield, New Jersey, the U.S.; The company is a leading provider of research service in the field of Next Generation Sequencing, Sanger DNA sequencing, sequencing of bacteria and phage, gene synthesis, DNA cloning, genomics including mutation analysis, single nucleotide polymorphism, and bioservices. GENEWIZ, Inc. has its geographic presence in U.S., China, Germany, France, Japan, and the U.K.</p><p><strong>9.&nbsp;<a href="https://www.genomics.cn/">Beijing Genomics Institute (China)</a></strong></p><p>Beijing Genomics Institute (BGI) is the world&rsquo;s largest genomics organization and non-profit research institution that was founded in 1999 and is headquartered in Shenzhen, China. The Company provides a wide range of commercial next generation sequencing services and genetic tests for medical institutions, agricultural and environmental applications. The Company operates all across the globe through its subsidiaries, namely, BGI China (Mainland), BGI Asia Pacific, BGI Americas (North and South America) and BGI Europe (Europe and Africa).</p><p><strong>10.&nbsp;<a href="https://www.scigenom.com/">SciGenom Labs Pvt. Ltd (India)</a></strong></p><p>SciGenom Labs Pvt. Ltd was founded in 2010 and is headquartered in Cochin, India with offices in Chennai &amp; Hyderabad in India, and San Francisco in the U.S. It is a Genomics R&amp;D services company that provides genomic sequencing and NGS services to life sciences and healthcare businesses globally as well as academic and government institutions in India.</p><p>Popular mentions &ndash; MedGenome (India), DNA Link, Inc. (South Korea), Otogenetics Corporation (U.S.), Novogene Corporation (China), LGC Limited (U.K.), CD Genomics (U.S.), SeqLL, LLC (U.S.)</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/12995/national-center-for-bioinformatics-ncb</guid>
  <pubDate>Wed, 23 Jul 2014 14:10:49 -0500</pubDate>
  <link></link>
  <title><![CDATA[National Center for Bioinformatics (NCB)]]></title>
  <description><![CDATA[
<p>NCB is offering M.Phil and Ph.D programs in the area of Bioinformatics. The major goal of NCB is to promote quality training and research in the area of Bioinformatics. Bioinformatics originated as a cross-disciplinary field as the need for computational sections to research problem raised in biomedicine. </p>

<p>More at http://ncb.qau.edu.pk/</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43828/understanding-hifi-reads</guid>
	<pubDate>Thu, 24 Mar 2022 19:48:11 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43828/understanding-hifi-reads</link>
	<title><![CDATA[Understanding HiFi Reads !]]></title>
	<description><![CDATA[<p><span>While little public data is available for either of the new synthetic long read approaches, Illumina showed an example comparison earlier this year at the&nbsp;</span><a href="https://www.festivalofgenomics.com/rami-mehio" target="_blank">Festival of Genomics &amp; Biodata conference</a><span>&nbsp;(FoG 2022). In the IGV screenshot presented (below), synthetic Infinity reads &ndash; labeled &ldquo;Longas&rdquo; &ndash; are at the top, followed by standard Illumina short reads, and PacBio HiFi reads labeled &ldquo;CCS&rdquo; depicted at the bottom:</span></p><p>Address of the bookmark: <a href="http://pacb.com/blog/the-hifi-difference-true-long-reads-vs-synthetic-long-reads/" rel="nofollow">http://pacb.com/blog/the-hifi-difference-true-long-reads-vs-synthetic-long-reads/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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