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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27965?offset=50</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29603/statistical-for-biological-research</guid>
	<pubDate>Thu, 03 Nov 2016 04:59:48 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29603/statistical-for-biological-research</link>
	<title><![CDATA[Statistical for biological research]]></title>
	<description><![CDATA[<p>There is no disputing the importance of statistical analysis in biological research, but too often it is considered only after an experiment is completed, when it may be too late.</p>
<p>This collection highlights important statistical issues that biologists should be aware of and provides practical advice to help them improve the rigor of their work.</p>
<p><em>Nature Methods</em>' <strong><a href="http://www.nature.com/collections/qghhqm/pointsofsignificance">Points of Significance</a></strong> column on statistics explains many key statistical and experimental design concepts. <strong><a href="http://www.nature.com/collections/qghhqm/resources">Other resources</a></strong> include an online plotting tool and links to statistics guides from other publishers.</p><p>Address of the bookmark: <a href="http://www.nature.com/collections/qghhqm" rel="nofollow">http://www.nature.com/collections/qghhqm</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29628/links</guid>
	<pubDate>Fri, 04 Nov 2016 06:19:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29628/links</link>
	<title><![CDATA[LINKS]]></title>
	<description><![CDATA[<p>LINKS is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, another draft genomes, etc)</p>
<p>Paper at&nbsp;https://gigascience.biomedcentral.com/articles/10.1186/s13742-015-0076-3</p><p>Address of the bookmark: <a href="https://github.com/warrenlr/LINKS/" rel="nofollow">https://github.com/warrenlr/LINKS/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29644/junior-research-fellow-at-rajiv-gandhi-centre-for-biotechnology-thiruvananthapuram</guid>
  <pubDate>Mon, 07 Nov 2016 10:27:06 -0600</pubDate>
  <link></link>
  <title><![CDATA[Junior Research Fellow at Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram]]></title>
  <description><![CDATA[
<p>Adv. # 22/ 2016<br />Applications are invited from suitable candidates for one position of Junior Research Fellow in a DST funded bioinformatics research project entitled "Major gene influxes in microbial genome evolution" in the Laboratory of Dr. Shijulal Nelson-Sathi at Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram.</p>

<p>ESSENTIAL QUALIFICATIONS:<br />We are looking for a motivated candidate with keen interest in bioinformatics and microbial genome evolution. The candidate must have a Master’s Degree in Bioinformatics, Computational Biology, Computer Science, Microbiology, Biology or a related field with good academic record.</p>

<p>DESIRABLE QUALIFICATIONS<br />Hands on research experience on handling next generation sequencing data and phylogenetic reconstruction methods. Excellent programming skills (Perl/Python/Java/Php) and experience in working on Unix/Linux platform is preferred. Furthermore; good knowledge is required in statistics (R/Matlab) and the application of bioinformatics analysis tools.</p>

<p>AGE:<br />Below 28 years as on 15th November, 2016.</p>

<p>EMOLUMENTS:<br />Rs. 25,000 + 20% HRA for NET/GATE qualified and Post Graduate in Professional Degree course qualified candidates and <br />Rs. 12,000/- + 20% HRA for others.</p>

<p>DURATION:<br />Initial appointment will be given for one year and further extension will be based on the performance till termination of the project.<br />Only those fulfilling the above criteria need apply and will be called for interview. In the event of more than 10 candidates being short-listed by screening the applications, a written test will be conducted before the selection interview and only those who are successful in the written test will be interviewed. No TA/ DA will be given for appearing in the interview.</p>

<p>Suitably qualified candidates may send applications in the prescribed format (Download here) with a photograph, a copy of full resume indicating the percentage of Marks obtained and attested photocopies of credentials &amp; experience to reach the undersigned on or before 15th November, 2016. Envelopes must be superscripted with abbreviated title of the project, advertisement number and job title. Selection to the position will not entitle the candidate to any future positions at RGCB (permanent or otherwise). As with all project positions at RGCB, the position will be co terminus with end of the project.</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29658/bookmarks-biostatistics-materials-and-books</guid>
	<pubDate>Tue, 08 Nov 2016 07:42:42 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29658/bookmarks-biostatistics-materials-and-books</link>
	<title><![CDATA[Bookmarks Biostatistics materials and books]]></title>
	<description><![CDATA[<p>Biostatistics did not spring fully formed from the brow of R. A. Fisher, but evolved over many years. This process is continuing, although it may not be obvious from the outside. It has been ten years since the first edition of this book appeared (and rather longer since it was begun). Over this time, new areas of biostatistics have been developed and emphases and interpretations have changed</p>
<p>Please bookmarks your favourate biostatistics&nbsp;books in commend sectons ...</p><p>Address of the bookmark: <a href="http://www.cos.ufrj.br/~bioestatistica/livros/Introduction%20to%20Biostatistics.pdf" rel="nofollow">http://www.cos.ufrj.br/~bioestatistica/livros/Introduction%20to%20Biostatistics.pdf</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29842/research-assistant-bioinformatics-recruitment-in-national-institute-of-cancer-prevention-research-icmr-on-contract-basis</guid>
  <pubDate>Tue, 15 Nov 2016 17:15:48 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Assistant Bioinformatics recruitment in National Institute Of Cancer Prevention &amp; Research (ICMR) on Contract basis]]></title>
  <description><![CDATA[
<p>National Institute Of Cancer Prevention &amp; Research - ICMR</p>

<p>Research Assistant Bioinformatics recruitment in National Institute Of Cancer Prevention &amp; Research (ICMR) on Contract basis <br />Project entitled: “Next generation EGFR inhibitor identification using ligand based QSAR technique” </p>

<p>Essential: M.Sc. in Bioinformatics or related field. Desirable: Experience in QSAR and structure based drug designing.<br />Age: 28 years<br />No.of Post: 1</p>

<p>Pay Scale : Rs.27000</p>

<p>Application format is attached and should be sent by post to Dr. Subhash M Agarwal, Scientist D, Division of Bioinformatics, National Institute of Cancer Prevention &amp; Research (ICMR), Plot No. I-7, Sector-39, Noida 201301 (U.P).</p>

<p>More at http://www.icmr.nic.in/icmrnews/NICPR_Advertisement%20for%20RA.pdf</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29912/maq-mapping-and-assembly-with-quality</guid>
	<pubDate>Tue, 22 Nov 2016 04:51:39 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29912/maq-mapping-and-assembly-with-quality</link>
	<title><![CDATA[Maq: Mapping and Assembly with Quality]]></title>
	<description><![CDATA[<p><strong>Maq</strong>&nbsp;stands for&nbsp;<em>Mapping and Assembly with Quality</em>&nbsp;It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by&nbsp;<a href="http://sourceforge.net/">SourceForge.net</a>. The project page is available at<a href="http://sourceforge.net/projects/maq/">http://sourceforge.net/projects/maq/</a>. Maq is previously known as mapass2.</p>
<h2>Run Maq Now</h2>
<p>Follow these steps to try Maq. All you need is a reference sequence file in the FASTA format.</p>
<ol>
<li>Prepare a reference sequence (ref.fasta). Better a bacterial genome.</li>
<li>Download maq, maq-data and maqview at the&nbsp;<a href="http://sourceforge.net/project/showfiles.php?group_id=191815">download page</a>.</li>
<li>Copy maq, maq.pl and maq_eval.pl to the $PATH or to the same directory.</li>
<li>Simulate diploid reference and read sequences, map reads, call variants and evaluate the results in one go:
<pre>maq.pl demo ref.fasta calib-30.dat
</pre>
where&nbsp;<em>calib-30.dat</em>&nbsp;is contained in maq-data.</li>
<li>View the alignment:
<pre>cd maqdemo/easyrun;
maqindex -i -c consensus.cns all.map;
maqview -c consensus.cns all.map</pre>
</li>
</ol>
<p><strong>Even for advanced maq users, running `maq.pl demo' is recommended. You may find something helpful.</strong></p><p>Address of the bookmark: <a href="http://maq.sourceforge.net" rel="nofollow">http://maq.sourceforge.net</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29995/hga</guid>
	<pubDate>Tue, 29 Nov 2016 07:25:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29995/hga</link>
	<title><![CDATA[HGA]]></title>
	<description><![CDATA[<p>HGA tool version 1.0 This tool helps to apply the Hierarchical Genome Assembly (HGA) method. The tool will apply: 1. Partitioning a given reads dataset into a given number of partitions. 2. Assembling each partitions using a pre-specified assembler (Velvet or SPAdes in this version) and using a given kmer size. 3. Merging all the assemblies of the partition. 4. Combining all the assemblies of the partition (using velvet with kmer value of 31). 5. Finaly, re-assembling the whole dataset with the merged contigs or the combined contigs, using a given kmer size.</p>
<p>https://github.com/aalokaily/Hierarchical-Genome-Assembly-HGA</p><p>Address of the bookmark: <a href="https://github.com/aalokaily/Hierarchical-Genome-Assembly-HGA" rel="nofollow">https://github.com/aalokaily/Hierarchical-Genome-Assembly-HGA</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30015/scripts</guid>
	<pubDate>Wed, 30 Nov 2016 10:35:15 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30015/scripts</link>
	<title><![CDATA[Scripts]]></title>
	<description><![CDATA[<p>Useful script for NGS analysis.</p><p>Address of the bookmark: <a href="http://augustus.gobics.de/binaries/scripts/" rel="nofollow">http://augustus.gobics.de/binaries/scripts/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30203/e-rga-enhanced-reference-guided-assembly-of-complex-genomes</guid>
	<pubDate>Mon, 19 Dec 2016 05:56:14 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30203/e-rga-enhanced-reference-guided-assembly-of-complex-genomes</link>
	<title><![CDATA[e-RGA: enhanced Reference Guided Assembly of Complex Genomes]]></title>
	<description><![CDATA[<p><span>Next Generation Sequencing has totally changed genomics: we are able to produce huge amounts of data at an incredibly low cost compared to Sanger sequencing. Despite this, some old problems have become even more difficult, de novo assembly being on top of this list. Despite efforts to design tools able to assemble, de novo, an organism sequenced with short reads, the results are still far from those achievable with long reads. In this paper, we propose a novel method that aims to improve de novo assembly in the presence of a closely related reference. The idea is to combine de novo and reference-guided assembly in order to obtain enhanced results.</span></p><p>Address of the bookmark: <a href="http://journal.embnet.org/index.php/embnetjournal/article/view/208" rel="nofollow">http://journal.embnet.org/index.php/embnetjournal/article/view/208</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30085/fqtools</guid>
	<pubDate>Thu, 08 Dec 2016 09:31:12 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30085/fqtools</link>
	<title><![CDATA[fqtools]]></title>
	<description><![CDATA[<p><code>fqtools</code><span>&nbsp;is a software suite for fast processing of&nbsp;</span><code>FASTQ</code><span>&nbsp;files. Various file manipulations are supported. See below for a full list of the subcommands available and a brief description of their purpose. Most of the individual subcommands will take either a single file or a pair of files as input. If no input file is specified, fqtools will attempt to read data from&nbsp;</span><code>stdin</code><span>. In this case, it is advisabe to specify the format of the data provided. For subcommands that generate FASTQ data, either a single file or a pair of files will be generated. If no&nbsp;</span><code>-o</code><span>&nbsp;argument is provided, single files will be writted to&nbsp;</span><code>stdout</code><span>.</span></p><p>Address of the bookmark: <a href="https://github.com/alastair-droop/fqtools" rel="nofollow">https://github.com/alastair-droop/fqtools</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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