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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/36880?offset=940</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37835/variantbam-filtering-and-profiling-of-next-generational-sequencing-data-using-region-specific-rules</guid>
	<pubDate>Thu, 04 Oct 2018 16:30:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37835/variantbam-filtering-and-profiling-of-next-generational-sequencing-data-using-region-specific-rules</link>
	<title><![CDATA[VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules]]></title>
	<description><![CDATA[<p>VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store only those read-pairs or reads who intersect some region around the variant locations. Alternatively, if your scientific question is focused on only one aspect of the data (e.g. breakpoints), many reads can be removed without losing the information relevant to the problem.</p>
<h5>&nbsp;</h5><p>Address of the bookmark: <a href="https://github.com/broadinstitute/VariantBam" rel="nofollow">https://github.com/broadinstitute/VariantBam</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/23378/ra-bioinformatics-at-bharathidasan-university</guid>
  <pubDate>Fri, 17 Jul 2015 19:40:45 -0500</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at Bharathidasan University]]></title>
  <description><![CDATA[
<p>Applications are invited from individuals who have high motivation to do research for the DBT sponsored project o n “Establishment of National Repository for Microalgae &amp; Cyanobacteria” funded by Department of Biotechnology, Govt. of India under the supervision of Dr. N. Thajuddin, Principal Investigator, Department of Microbiology, Bharathidasan University, Tiruchirappalli- 620 024.</p>

<p>1. Research Associate – 1 No.</p>

<p>Rs. 36,000/38,000/40,000 per month for I, II and III year + 20% HRA</p>

<p>Essential : Doctoral degree in relevant subject from recognized University/ Institutes</p>

<p>Desirable: Research experience in molecular biology and bioinformatics.</p>

<p>Interested candidates can send their complete CV in plain paper with a passport size photograph, with details of marks secured in all subjects from plus two stage (with proof, full postal address, sex, date of birth, community etc., along with additional qualification or experiences and two address of references whom could be contacted.</p>

<p>DEPARTMENT OF MICROBIOLOGY SCHOOL OF LIFE SCIENCES UNIVERSITY Dr. N. THAJUDDIN Professor &amp; Head Dean, Faculty of Science, Technology &amp; Engineering Tiruchirappalli – 620 024, India, Phone: +91 431 2407082; Mobile +91 098423 79719; E-mail: nthaju2002@yahoo.com</p>

<p>Application should reach the Principal Investigator on or before 5.8.2015 by Speed post/Couriers/Email (nthaju2002@yahoo.com), with subject printed as “Application for Research Associate /Technical Assistant /Lab attendant” in the envelop. Qualifying candidates will be short listed and communicated with date of interview. No TA and DA will be given for attending the interview. Address for Communication Dr.N.Thajuddin Principal Investigator Department of Microbiology Bharathidasan University Tiruchirappalli – 620 024, Tamil Nadu.</p>

<p>Advertisement: www.bdu.ac.in/adv/microbiology_advt.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39726/jackalope-a-swift-versatile-phylogenomic-and-high-throughput-sequencing-simulator</guid>
	<pubDate>Fri, 26 Jul 2019 00:58:12 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39726/jackalope-a-swift-versatile-phylogenomic-and-high-throughput-sequencing-simulator</link>
	<title><![CDATA[jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator]]></title>
	<description><![CDATA[<p><code>jackalope</code> simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations&mdash;the latter of which can include selection, recombination, and demographic fluctuations. <code>jackalope</code> can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written to standard file formats.</p>
<p><span>A swift, versatile phylogenomic and high-throughput sequencing simulator </span> <span><a href="https://jackalope.lucasnell.com">https://jackalope.lucasnell.com</a></span></p><p>Address of the bookmark: <a href="https://github.com/lucasnell/jackalope" rel="nofollow">https://github.com/lucasnell/jackalope</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/23428/icgeb-bioinformatics-research-associate-vacancy</guid>
  <pubDate>Thu, 23 Jul 2015 19:45:16 -0500</pubDate>
  <link></link>
  <title><![CDATA[ICGEB Bioinformatics Research Associate Vacancy]]></title>
  <description><![CDATA[
<p>Junior Research Fellow (JRF) / Postdoc positions in Cell and Structural biology at ICGEB, New Delhi with Amit Sharma</p>

<p>Research positions are open starting 15th August 2015.</p>

<p>Projects are specifically for protein structure analysis. Projects also involve drug binding studies both computationally and experimentally.</p>

<p>CSIR/SPM/INSPIRE/DBT/UGC JRF/post-doc fellowships are essential for applications.</p>

<p>Email curriculum vitae to sb.icgeb@gmail.com by 14 August 2015</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links</guid>
	<pubDate>Thu, 13 Feb 2020 00:20:00 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links</link>
	<title><![CDATA[genomics public data links !]]></title>
	<description><![CDATA[<p>List of publically available databases on google server.</p>
<p>More at <a href="https://software.broadinstitute.org/gatk/download/bundle">https://software.broadinstitute.org/gatk/download/bundle</a></p>
<p><a href="ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/">ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/</a>.</p>
<p><a href="ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/">ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/</a></p><p>Address of the bookmark: <a href="https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1" rel="nofollow">https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/23578/srf-post-in-nehu-shillong</guid>
  <pubDate>Tue, 04 Aug 2015 03:17:05 -0500</pubDate>
  <link></link>
  <title><![CDATA[SRF post in NEHU, Shillong]]></title>
  <description><![CDATA[
<p>Bioinformatics Centre (DIC)<br />NORTH-EASTERN HILL UNIVERSITY<br />SHILLONG 793022</p>

<p>Applications with complete bio-data from candidates possessing the required qualifications are invited for the posts of JRF (1) and Project Assistant (1) in DBT, GOI-funded research project “Next Generation Sequencing (NGS)- based de novo assembly of expressed transcripts and genome information of Orchids in North-East India” in DBT’s Twinning programme for NE as per DBT sanction order and norms.</p>

<p>(i) JRF(1 no.):</p>

<p>Qualifications: M.Tech/M.Sc in Life Sciences/ Botany/ Zoology/ Biochemistry/ Biotechnology/ Bioinformatics;</p>

<p>Desirable: Aptitude for Bioinformatics and Computer Programming/ Next generation sequencing data analysis</p>

<p>(ii) Project Assistant (1 no.):</p>

<p>Qualifications: Graduation in Science,</p>

<p>Desirable: Experience of working in a Life Science/Plant Biotechnology lab. and familiarity with computers and field work viz. collection of samples.</p>

<p>The applications through email bicnehu@gmail.com or post must reach the undersigned within 15 days from the date of publication of this advertisement. The advertised posts are purely temporary for the duration of the project and subject to availability of the funds from DBT. The appointment does not confer any entitlement or right over the posts for absorption in the University service. Prof. Pramod Tandon, PI/Mr. Devendra Kumar Biswal (Co-PI) email: bicnehu@gmail.com</p>

<p>Advertisement: www.nehu.ac.in/Advertisements/BIC_AdvtPV_030815.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34445/inc-seq-accurate-single-molecule-reads-using-nanopore-sequencing</guid>
	<pubDate>Mon, 27 Nov 2017 10:38:56 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34445/inc-seq-accurate-single-molecule-reads-using-nanopore-sequencing</link>
	<title><![CDATA[INC-Seq: accurate single molecule reads using nanopore sequencing]]></title>
	<description><![CDATA[<p><span>INC-Seq reads enabled accurate species-level classification, identification of species at 0.1&nbsp;% abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.</span></p><p>Address of the bookmark: <a href="https://github.com/CSB5/INC-Seq" rel="nofollow">https://github.com/CSB5/INC-Seq</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/23782/bioinformatics-openings-at-jnu</guid>
  <pubDate>Sun, 16 Aug 2015 01:03:11 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics openings at JNU]]></title>
  <description><![CDATA[
<p>School of Biotechnology<br />JAWAHARLAL NEHRU UNIVERSITY<br />NEW DELHI</p>

<p>Jawaharlal Nehru University has been granted funds by the Department of Biotechnology (DBT), Govt. of India to initiate an Inter-School programme in JNU to strengthen training and research called "DBT-Jawaharlal Nehru University, New Delhi-Interdisciplinary Life Science Programme for Advanced Research and education" with the broad project area entitled "From Molecules to Systems: Exploring biological space using chemical and synthetic biology" cutting across Physical, Chemical and Biological Sciences.</p>

<p>Applications are invited for the following purely temporary posts at various levels in the various Group projects for Research and Technical positions. The project is upto March 2017, but the appointments shall be initially for a period of one year, renewable every year depending on the performance of project staff:</p>

<p>Project Sub-Title: Synthetic Genomics: Making sense out of 'junk' DNA</p>

<p>Senior Research Fellow (SRF) - 01 Post</p>

<p>Qualifications: M.Sc in Bioinformatics, with minimum 2 year research experience, specialization in microRNA, molecular modelling, systems and/or Synthetic biology with publication in the relevant area would be desirable.</p>

<p>Investigator: Prof. Pawan Kumar Dhar</p>

<p>Fellowship: Rs. 14000+30% HRA p.m.</p>

<p>Project Sub-Title: "Structure, function, and dynamics of biomolecules and Molecular engineering"</p>

<p>Postdoctoral Fellow (PDF) - 01 Post</p>

<p>Essential Qualifications: PhD in Science(Bioinformatics/Computational Biology, Physics, Chemistry, Mathematics, &amp; Statistics), specialized in the area of Computational Biology/Structural Bioinformatics/ Quantum Chemistry/Molecular Dynamics &amp; Simulation /Systems Biology , reflected by thesis topics and or publication of papers during PhD and/or Post doctoral experience.</p>

<p>Desirable Qualifications: Computational methods and designing experience in the field of Structure based or ligand based drug design, Chemoinformatics, Programming capabilities as required for developing tools in the computational &amp; systems Biology.</p>

<p>Investigator: Prof. Indira Ghosh, SCIS</p>

<p>Salary: Rs. 22, 000 + 30% HRA</p>

<p>(Note: Revised emoluments shall be payable if Educational Qualifications or Eligibility Criteria as per DST OM No. A.20020/11/97-IFD dated 31-03-2010 are met by the research personnel)</p>

<p>The applications on plain paper indicating name, date of birth/age, address, essential / technical / professional qualifications, experience, research work, should reach the Programme Coordinator on or before 27th August 2015 at the following address:</p>

<p>The Envelop should be marked for the Post applied for. Any clarifications regarding projects may be sought from the respective project investigators as mentioned.</p>

<p>Address for correspondence:<br />Programme Coordinator<br />DBT-JNU BUILDER programme<br />School of Biotechnology<br />Jawaharlal Nehru University<br />New Delhi 110067</p>

<p>More at http://www.jnu.ac.in/career/currentjobs.htm</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</guid>
	<pubDate>Mon, 30 Apr 2018 04:38:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</link>
	<title><![CDATA[ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.]]></title>
	<description><![CDATA[<p><span>ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.&nbsp;</span></p>
<p><span>Detail paper at&nbsp;https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8</span></p><p>Address of the bookmark: <a href="https://github.com/VicugnaPacos/ALPACA" rel="nofollow">https://github.com/VicugnaPacos/ALPACA</a></p>]]></description>
	<dc:creator>Seema Singh</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/24462/icar-project-ra-position-institute-of-bioinformatics-iob-bangalore</guid>
  <pubDate>Tue, 22 Sep 2015 23:41:31 -0500</pubDate>
  <link></link>
  <title><![CDATA[ICAR project RA position @ Institute of Bioinformatics (IOB) Bangalore]]></title>
  <description><![CDATA[
<p>Applications are invited for the post of Research Associate (RA) in the ICAR project on "Lactation stress associated postpartum anestrus SNP array in buffaloes". We are looking for a motivated candidate for handling Next Generation sequencing data analysis with a strong background in bioinformatics and programming.</p>

<p>The position is open for immediate appointment and available for two years and then extendable for additional one year. The applicant will be appointed as Research Associate based on qualifications as detailed below:</p>

<p>Research Associate:</p>

<p>-Master’s degree with bioinformatics with at least 2 years of research experience in Next Generation sequencing data analysis as evidence from Fellowship/ Associateship / Training / other engagements.</p>

<p>-Familiarity with bioinformatics tools, database development, programming skills</p>

<p>-Minimum 1 publication in any peer reviewed journal</p>

<p>Salary will be as per ICAR rules and guidelines. Application will be shortlisted based on CV, reference letters from mentors and telephonic interview. Candidates will be called for a personal interview at Bangalore before appointment. No travel expense will be provided for attending interview at Bangalore.</p>

<p>Interested candidates may send a Letter of Interest and CV by email to: keshav@ibioinformatics.org before September 29, 2015.</p>
]]></description>
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