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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30236?offset=1490</link>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22580/appointment-of-two-traineeships-and-two-studentships-in-bioinformatics</guid>
  <pubDate>Wed, 10 Jun 2015 10:19:07 -0500</pubDate>
  <link></link>
  <title><![CDATA[Appointment of two traineeships and two studentships in Bioinformatics]]></title>
  <description><![CDATA[
<p>Jawaharlal Nehru<br />TROPICAL BOTANIC GARDEN AND RESEARCH INSTITUTE<br />An organization under the Kerala State Council for Science, Technology and Environment and<br />National Centre of Excellence, Government of India<br /> <br />Applications are invited for the appointment of two traineeships and two studentships in Bioinformatics for a period of six months sponsored by Department of Biotechnology, Government of India in the Bioinformatics Sub-DIC, Saraswathy Thangavelu Centre, JNTBGRI, Puthenthope, Thiruvananthapuram 695 586. The required qualifications and other details are given below.</p>

<p>Monthly fellowship (in rupee): 5,000/-<br />	<br />Traineeship<br />	<br />First Class M.Sc Bioinformatics/ Biotechnology/ Botany<br />	<br />Studentship: 5,000/-<br />	<br />M.Phil/M.Tech Bioinformatics/ Biotechnology/ any branch of Life Science students for doing their thesis work in the area of Bioinformatics.</p>

<p>Age limit as on 1.1.2015, 28 years. Age relaxation will be provided for SC, ST, OBC candidates as per Govt. norms.</p>

<p>Interested candidates may appear for walk-in-interview on 16th June 2015 at 10.30 am at JNTBGRI, Palode, Thiruvananthapuram. The candidate should report to the Office at Palode before 10.00 am</p>

<p>More at http://www.jntbgri.in/jntbgri/news/File0001.pdf</p>
]]></description>
</item>
<item>
	<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>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22779/research-associate-at-international-centre-for-genetic-engineering-and-biotechnology-icgeb</guid>
  <pubDate>Wed, 17 Jun 2015 18:49:05 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate at International Centre for Genetic Engineering and Biotechnology (ICGEB)]]></title>
  <description><![CDATA[
<p>Research Associate<br />International Centre for Genetic Engineering and Biotechnology (ICGEB)<br />Address: Aruna Asaf Ali Marg, Jawaharlal Nehru University, New Delhi<br />Postal Code: 110067<br />City: New Delhi<br />State: Delhi<br />Qualifications: Experience in many docking softwares and operating systems is essential. Additional experience in bioinformatics and computational biology tools will be useful.<br />Details will be available at: http://www.icgeb.org/vacancies.html<br /> <br />How To Apply: Submit curriculum vitae to: sb.icgeb@gmail.com<br />Last Date: 5 July 2015</p>
]]></description>
</item>
<item>
	<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>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22788/research-associate-bioinformatics-job-position-in-indian-agricultural-statistics-research-institute-iasri-pusa-new-delhi</guid>
  <pubDate>Wed, 17 Jun 2015 20:48:40 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate Bioinformatics job position in Indian Agricultural Statistics Research Institute (IASRI), Pusa, New Delhi]]></title>
  <description><![CDATA[
<p>Research Associate Statistics</p>

<p>Eligibility : M Phil / Phd, MSc</p>

<p>Location : Delhi</p>

<p>Last Date : 27 Jun 2015</p>

<p>Hiring Process : Walk - In<br />Indian Agricultural Statistics Research Institute (IASRI) - Job DetailsDate of posting:03 Jun 15</p>

<p>Research Associate Statisticsjob position in Indian Agricultural Statistics Research Institute (IASRI)<br />on purely contractual temporary basis</p>

<p>Project : “ICAR-Network Project of Transgenic in Crops”</p>

<p>Qualification : Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent OR Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent with 1st Division or 60% marks or equivalent with at least two years of research experience.</p>

<p>No.of Post: 01</p>

<p>Emoluments for RA: Consolidated Rs. 24000/- per month + 30% HRA for Ph.D holders and consolidated Rs. 23000/- per month + 30% HRA for Master Degree.</p>

<p>Age Limit : 40 years<br />How to apply</p>

<p>Walk-in-interview will be held on 27th June 2015, 10.30 A.M at IASRI, Pusa, New Delhi</p>

<p>More at http://iasri.res.in/employment/employment.htm</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39441/snakepipes-a-toolkit-based-on-snakemake-and-python-for-analysis-of-ngs-data</guid>
	<pubDate>Thu, 30 May 2019 04:06:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39441/snakepipes-a-toolkit-based-on-snakemake-and-python-for-analysis-of-ngs-data</link>
	<title><![CDATA[snakepipes: A toolkit based on snakemake and python for analysis of NGS data]]></title>
	<description><![CDATA[<p><span><span>snakePipes are flexible and powerful workflows built using&nbsp;</span><a href="https://github.com/maxplanck-ie/snakepipes/blob/master/snakemake.readthedocs.io">snakemake</a><span>&nbsp;that simplify the analysis of NGS data.</span></span></p>
<ul>
<li>DNA-mapping*</li>
<li>ChIP-seq*</li>
<li>RNA-seq*</li>
<li>ATAC-seq*</li>
<li>scRNA-seq</li>
<li>Hi-C</li>
<li>Whole Genome Bisulfite Seq/WGBS</li>
</ul>
<p><span>(*Also available in "allele-specific" mode)</span></p>
<p><span>snakePipes can be installed via conda : </span></p>
<p><span>'conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'. </span></p>
<p><span>Source code (</span><a href="https://github.com/maxplanck-ie/snakepipes" target="">https://github.com/maxplanck-ie/snakepipes</a><span>) and documentation (</span><a href="https://snakepipes.readthedocs.io/en/latest/" target="">https://snakepipes.readthedocs.io/en/latest/</a><span>) are available online.</span></p><p>Address of the bookmark: <a href="https://github.com/maxplanck-ie/snakepipes" rel="nofollow">https://github.com/maxplanck-ie/snakepipes</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22944/icgeb-bioinformatics-research-associate-vacancy</guid>
  <pubDate>Thu, 25 Jun 2015 20:41:00 -0500</pubDate>
  <link></link>
  <title><![CDATA[ICGEB Bioinformatics Research Associate Vacancy]]></title>
  <description><![CDATA[
<p>Research Associate Position at ICGEB, New Delhi with Dr. Amit Sharma</p>

<p>Starting 15th July 2015, the position relates to a project specifically for in silico drug docking, screening, design, optimisation and linkage with active chemists. </p>

<p>Experience in many docking softwares and operating systems is essential. </p>

<p>Additional experience in bioinformatics and computational biology tools will be useful. </p>

<p>Submit curriculum vitae to: sb.icgeb@gmail.com</p>

<p>Closing date: 5 July 2015</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40604/gapfinisher-a-reliable-gap-filling-pipeline-for-sspace-longread-scaffolder-output</guid>
	<pubDate>Fri, 24 Jan 2020 06:04:40 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40604/gapfinisher-a-reliable-gap-filling-pipeline-for-sspace-longread-scaffolder-output</link>
	<title><![CDATA[gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output]]></title>
	<description><![CDATA[<p><span>gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser. </span></p>
<p><span>gapFinisher can fill gaps in draft genomes quickly and reliably.</span></p><p>Address of the bookmark: <a href="https://github.com/kammoji/gapFinisher" rel="nofollow">https://github.com/kammoji/gapFinisher</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/23384/research-scientist-at-dupont</guid>
  <pubDate>Fri, 17 Jul 2015 20:36:17 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Scientist at DuPONT]]></title>
  <description><![CDATA[
<p>Research Scientist<br />Hyderabad, Telangana<br />Job Description</p>

<p>Job Description</p>

<p>The Global Trait Discovery Informatics (GTDI) group located at the DuPont Knowledge Centre (DKC), Hyderabad, India is currently seeking applications for a highly motivated computational biologist. The GTDI group contributes to research programs in plant biotechnology at the DKC as well as across research centers located in DuPont Pioneer, Johnston, Iowa and at the DuPont Experimental Station in Wilmington, Delaware.</p>

<p>We are looking for candidates who have experience in analysis of high-throughput -omics datasets. The researcher will be primarily responsible for analyzing diverse -omics datatypes, such as transcriptomics, proteomics and metabolomics and actively contribute towards building streamlined solutions.</p>

<p>The candidate will be part of a diverse team of experimental biologists, computational biologists and software developers. A critical aspect of this position involves working with global teams across multiple locations and will require effective project coordination and communication skills. This is an exciting opportunity for candidates with strong data driven skills, who want to work at the interface of computational and experimental biology and contribute towards scientific discovery.</p>

<p>Responsibilities</p>

<p>·Integrate and analyze multiple datatypes in the context of experimental observations with a goal towards formulating testable hypothesis.</p>

<p>·Understanding the research questions from experimental biologists and formulate relevant in silico analyses.</p>

<p>·Establish and implement systematic analysis workflows starting from processing of raw data to biological interpretation.</p>

<p>·Critically analyze a wide variety of experimental data with a view to solving the underlying research questions.</p>

<p>·Identify and generate datasets for scientific testing and evaluation of algorithms.</p>

<p>Qualifications</p>

<p>PhD in computational biology, bioinformatics, population genetics, complex systems, computer sciences or any relevant physical or mathematical sciences, with experience in analyzing diverse -omics datasets.</p>

<p>Job Qualifications</p>

<p>Qualifications</p>

<p>PhD in computational biology, bioinformatics, population genetics, complex systems, computer sciences or any relevant physical or mathematical sciences, with experience in analyzing diverse -omics datasets.</p>

<p>More at http://careers.dupont.com/jobsearch/job-details/research-scientist/006077W-01/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41730/parliament2-runs-a-combination-of-tools-to-generate-structural-variant-calls-on-whole-genome-sequencing-data</guid>
	<pubDate>Thu, 28 May 2020 21:57:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41730/parliament2-runs-a-combination-of-tools-to-generate-structural-variant-calls-on-whole-genome-sequencing-data</link>
	<title><![CDATA[Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome sequencing data]]></title>
	<description><![CDATA[<p>Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a region, Inversions of a region, or Translocations between two regions in the genome.</p>
<p>Parliament2 runs a combination of tools to generate structural variant calls on whole-genome sequencing data. It can run the following callers: Breakdancer, Breakseq2, CNVnator, Delly2, Manta, and Lumpy. Because of synergies in how the programs use computational resources, these are all run in parallel. Parliament2 will produce the outputs of each of the tools for subsequent investigation.</p><p>Address of the bookmark: <a href="https://github.com/dnanexus/parliament2" rel="nofollow">https://github.com/dnanexus/parliament2</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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