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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/29384?offset=1400</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38169/amstat-display-statistics-of-large-sequence-files-from-next-generation-sequencing-projects</guid>
	<pubDate>Fri, 09 Nov 2018 13:34:56 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38169/amstat-display-statistics-of-large-sequence-files-from-next-generation-sequencing-projects</link>
	<title><![CDATA[AMStat: display statistics of large sequence files from next generation sequencing projects]]></title>
	<description><![CDATA[<p><span>SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to&nbsp;</span><a href="http://samstat.sourceforge.net/#about">SAM/BAM</a><span>&nbsp;files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines.</span></p><p>Address of the bookmark: <a href="http://samstat.sourceforge.net/" rel="nofollow">http://samstat.sourceforge.net/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/20677/postdoctoral-researcher-at-department-of-biotechnology-catholic-university-of-daegu-kyungsan-kyungbuk-south-korea</guid>
  <pubDate>Thu, 29 Jan 2015 12:11:16 -0600</pubDate>
  <link></link>
  <title><![CDATA[Postdoctoral Researcher at Department of Biotechnology, Catholic University of Daegu, Kyungsan, Kyungbuk, South Korea.]]></title>
  <description><![CDATA[
<p>Applications are invited from Indian nationals for a Post Doctoral position at Molecular Medical Laboratory, Department of Biotechnology, Catholic University of Daegu, Kyungsan, Kyungbuk, South Korea.</p>

<p>Qualification required: PhD in Life Sciences/ Molecular Biology/ Bioinformatics or related discipline.</p>

<p>Desirable Qualification:</p>

<p>1. Candidates having experience in molecular biology techniques and must be well versed with bioinformatics tool or expert in relevant fields will be preferred.<br />2. The candidate should have good communication skill, knowledge about designing experiments and analyzing data.<br />3. Sense of initiative, autonomy, organization and thoroughness, good relation qualities.<br />Remuneration: 2000USD per month.</p>

<p>Last date of submitting the complete applications furnishing Bio-data is 10th February, 2015.</p>

<p>Interested candidates should send their resume including all personal as well as academic details to the principal investigator Prof Seung-Won Park (email:microsw@cu.ac.kr)</p>

<p>The shortlisted candidates will be intimated within February 2015.</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42418/scientist-b-bioinformatics-at-aiims-delhi</guid>
  <pubDate>Sun, 20 Dec 2020 04:34:55 -0600</pubDate>
  <link></link>
  <title><![CDATA[Scientist-B (Bioinformatics) at AIIMS, Delhi]]></title>
  <description><![CDATA[
<p>Name of the Project: “Artificial intelligence in Oncology, Harnessing big data and advanced computing to provide personalized diagnosis and treatment for Cancer patients”</p>

<p>Age Limit: 35</p>

<p>How to Apply for the AIIMS Life Science Job:</p>

<p>Interested applicants are asked to send out a detailed CV to Dr Ashok Sharma (aioncoaiims@gmail.com). Laboratory of Chromatin and also Cancer Epigenetics, Department of Biochemistry with the subject line “Application for Scientist-B position for MeitY project” latest by January 01st, 2021.<br />Complete Information of the year of passing, experience, marks, etc. ought to be mentioned in the CV Incomplete. applications will certainly be rejected Just shortlisted applicants will be called for interview. Chosen candidates will certainly be intimated by email/phone.<br />No TA/DA will certainly be paid for appearing in the interview.<br />Note, The institute reserved the right to fill up or not to fill up the post advertised.</p>

<p>Emoluments: Rs. 56,000/- plus 24 percent HRA</p>

<p>Eligibility:<br />2nd class Master’s Degree with a PhD in a pertinent subject (Bioinformatics) from.a recognized University<br />1st class Master’s degree in Life Sciences (Bioinformatics) from a recognized university OR.<br />Bachelor’s Degree in Engineering or-Technology with minimal 60% marks from a recognized University or equivalent.</p>

<p>Desirable Qualifications:<br />Experience in Bioinformatics/NGS data. Analysis/System Biology/Computer Science/ statistics with experience in Machine learning/Al project.<br />Experience of Deep learning applications in biological data ( image/text).<br />Proficient in Rf Python machine learning libraries.<br />Prior experience in the cancer-related project (ML-based) will be advantageous.<br />Experience with PyTorch/TensorFlow will certainly be very desirable.<br />Applicant should have strong scientific writing as well as. verbal abilities.<br />Papers in sci-indexed journals demonstrating ML skill sets.<br />Database handling will certainly be plus yet not required.</p>

<p>More detail at https://www.aiims.edu/images/pdf/recruitment/advertisement/biochem-16-12-20.pdf</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22438/research-associate-nbfgr-lucknow-uttar-pradesh</guid>
  <pubDate>Thu, 28 May 2015 19:37:22 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate NBFGR - Lucknow, Uttar Pradesh]]></title>
  <description><![CDATA[
<p>NBFGR, Lucknow is recruiting Bioinformatics experts for the post of Research Associate</p>

<p>Name of Position : Research Associate<br />No of Post : One<br />Desired candidate Profile : Candidate should be PhD in Bioinformatics or equivalent or Post-Graduation Bioinformatics with 1st division or 60% marks. Preference will be given to candidates having experience in server management<br />Remuneration : Rs 24000/- pm + HRA for PhD holders<br />Age requirement- 40 years (5 years relaxation for SC/ST/women candidates and 3 years for OBC candidates) as on date of interview.</p>

<p>How to apply- Interested candidates can walk -in-interview on 30.05.2015 at 10:00 hrs at National Bureau of Fish Genetic Resources, Lucknow.</p>

<p>Ref- http://www.nbfgr.res.in/PDF/News%20&amp;%20Events/Walk%20in%20interview%20on%2030.05.2015.pdf</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/41043/postdoctoral-scientist-genome-analytics-genome-bioinformatics-mf</guid>
  <pubDate>Sun, 16 Feb 2020 02:57:40 -0600</pubDate>
  <link></link>
  <title><![CDATA[Postdoctoral scientist genome analytics/ genome bioinformatics (m/f/*)]]></title>
  <description><![CDATA[
<p>https://www.uksh.de/jobs/Stellenangebote-nr-20190570-p-8.html<br />Your profile:<br />Degree in bioinformatics, biostatistics, or equivalent<br />Experience in the processing and analysis of large-scale genomics data using compute clusters / high-performance computing<br />Strong competence in working in Unix/Linux environments (shell)<br />Strong programming skills (in particular: Python, R, Perl)<br />Experience with using git and snakemake<br />Fluent English language skills, both spoken and written<br />Strong communication skills and motivation to work in a young, interdisciplinary, dynamic team</p>

<p>Additional Information:</p>

<p>If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).</p>

<p>Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).</p>

<p>Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.</p>

<p>Wir freuen uns auf Ihre Bewerbung bis zum 15.03.2020 unter Angabe unserer Ausschreibungsnummer 20190570.119.CL.</p>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21021/ra-bioinformatics-at-iiser</guid>
  <pubDate>Fri, 06 Feb 2015 04:05:49 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at IISER]]></title>
  <description><![CDATA[
<p>Advertisement: Research Position in Computational Biology in the group of Shree P. Pandey Positions available in the area of NGS data analysis, bioinformatics, plant genomics Project Description: Projects involves high throughput analysis of data mostly generated by massively parallel sequencing (RNA-Seq and small-RNA-Seq), microarrays and related platforms.</p>

<p>We are looking for highly motivated and bright individuals interested in high-throughput cutting-edge data analyses methods in genomics (computational positions). Available positions:</p>

<p>Applications are invited from suitable candidates in both, the Max Planck India Partner Program and the CRP Wheat Program for openings at the levels:</p>

<p>Minimum qualification Salary scale (per month)</p>

<p>Project assistant Bachelor’s / Master’s Rs. 10000 / Rs. 14000</p>

<p>Project fellow (junior data analyst) Masters + research experience Rs. 16000</p>

<p>Research fellow (senior data analyst) Masters + adequate research experience/desirable skill sets Rs. 22000</p>

<p>Research Associated PhD (&lt;1yr) / &gt; 1 yr experience Rs. 28000 / Rs. 32000</p>

<p>Condition to satisfactory performance, availability of funds and requirements of the project, the positions could be available upto a period of ~2 years (or funding of the project).</p>

<p>Essential qualification: MSc/BTech/MTech/PhD (or other suitable qualification) in discipline related to bioinformatics, computational biology, computer application (or equivalent)/ ‘Advance PostGraduate Diploma in Bioinformatics’. Proficiency in one of the programming languages or statistics (proficient in R for example) is compulsory.</p>

<p>Desirable qualification:</p>

<p>1. Programming experiences in at least one low level language such as C/C++ and one scripting language such as Perl/Python/PHP and knowledge of SQL/MySQL.</p>

<p>2. Substantial experience in the linux or other unix environments.</p>

<p>Application process: Applications should contain CV along with brief description (maximum 1 page) of research conducted (highlighting skills and experience) till now. Applications should be sent by email to Shree P. Pandey, Department of Biological Sciences, IISER-Kolkata, Mohanpur Campus, West Bengal within 2 weeks (Feb 19th 2015). E-mail: sppiiserkol@gmail.com, sppandey@iiserkol.ac.in Brief description of the group: We are an interdisciplinary group focusing on small-RNA (miRNA, siRNA) mediated regulation of signaling and defense. Project equally involve bioinformatics and systems biology (specially microarrays and next-generation sequencing (NGS) data analysis and its use), along with plant molecular biology, genetic engineering, field biology, and analytical plant chemistry for understanding response of plants to biotic stresses. For more details visit: http://www.iiserkol.ac.in/~sppandey/</p>

<p>Advertisement:</p>

<p>www.iiserkol.ac.in/images/iiserk/advertisements/advertisement_7_spp_feb_2015.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43892/choosing-the-right-ngs-sequencing-instrument-for-your-study</guid>
	<pubDate>Wed, 15 Jun 2022 00:37:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43892/choosing-the-right-ngs-sequencing-instrument-for-your-study</link>
	<title><![CDATA[Choosing the Right NGS Sequencing Instrument for Your Study]]></title>
	<description><![CDATA[<p>The right sequencing instrument for your study depends on your project goal. Setting aside turnaround time and price, it essentially comes down to the numbers of reads and read length you need for your experiment. Below, we've described and compared metrics for each of the instruments available. If you&rsquo;re new to high-throughput sequencing and have questions about how you should design your sequencing run, fill out our&nbsp;<a href="https://genohub.com/ngs-consultation/"><span>free consultation form</span></a>&nbsp;and we'll get in touch with you to help.</p>
<p>More at&nbsp;https://genohub.com/ngs-instrument-guide/</p><p>Address of the bookmark: <a href="https://genohub.com/ngs-instrument-guide/" rel="nofollow">https://genohub.com/ngs-instrument-guide/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21095/ra-walk-in-interview-actrec</guid>
  <pubDate>Mon, 09 Feb 2015 01:06:16 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA WALK-IN-INTERVIEW @ ACTREC]]></title>
  <description><![CDATA[
<p>No. ACTREC/Advt./ 7 /2015</p>

<p>Title of the Project<br />Research Associate<br />(One position)<br />DBTs Biotechnology/Bioinformatics training centre<br />PI Dr. Ashok Varma	</p>

<p>Duration of the Project Six Months from the date of appointment, can be extended further for six month.</p>

<p>Date &amp; Time: 17th February, 2015 at 10.00 a.m.</p>

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

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

<p>Ph.D. Degree in Basic Sciences from recognized University. Research experience in Bioinformatics or on gene cloning, protein purification, and crystallization.</p>

<p>*M.Sc. degree obtained after a one year course will not be considered.</p>

<p>Selected candidate will have to join at the earliest.</p>

<p>Consolidated Salary: Rs.28,600/- p.m. {Rs.22,000/- + 30% HRA}</p>

<p>The work progress of the candidate will be monitored and extension after 6 months will depend on satisfactory progress of the work.</p>

<p>Candidates fulfilling these requirements should pre-register by sending their application in the prescribed format with recent CV and contact details of 2 referees by e-mail to ‘program.office@actrec.gov.in’ latest by 17.00 hrs on 12-02-2015.<br />The interviews would be held on 17th February, 2015 and will be only for the pre-registered candidates. Candidates should report between 09.30 to 10.00 a.m. in Steno Pool, 3rd floor, Khanolkar Shodhika, ACTREC, Kharghar, Navi Mumbai.<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>All correspondence should be strictly made only to ‘program.office@actrec.gov.in’ as indicated.</p>

<p>Advertisement: www.actrec.gov.in/data%20files/2015/AV-RA-DBT-28-1-15.docx</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/44672/libraries-or-management-tools-for-high-throughput-sequencing-data</guid>
	<pubDate>Fri, 04 Oct 2024 02:45:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/44672/libraries-or-management-tools-for-high-throughput-sequencing-data</link>
	<title><![CDATA[Libraries or management tools for high throughput sequencing data]]></title>
	<description><![CDATA[<ul>
<li><a href="http://gatb.inria.fr/"><span>GATB</span></a>&nbsp;Library.&nbsp;The&nbsp;<span>Genome Analysis Toolbox with de-Bruijn graph.&nbsp;</span>A large part of tools developed by the GenScale team are based on this library.<br />These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (<em>e.g.</em>&nbsp;metagenomes). Among them are (the full is available here:&nbsp;<a href="https://gatb.inria.fr/software/">https://gatb.inria.fr/software/</a>):</li>
<li><a href="https://github.com/morispi/LRez"><span>LRez</span></a>: C++ Library and toolkit for the barcode-based management and indexation of linked-read datasets.</li>
</ul><h2>Variant calling and/or genotyping</h2><ul>
<li><a href="https://gatb.inria.fr/software/discosnp/" title="DiscoSNP">DiscoSNP++ and&nbsp;discoSnpRAD</a>: Reference-free small variant discovery (SNPs and indels)</li>
<li><a href="https://gatb.inria.fr/software/mind-the-gap/" title="MindTheGap">MindTheGap</a>: Detection and assembly of large insertion variants</li>
<li><a href="https://gatb.inria.fr/software/takeabreak/" title="TakeABreak">TakeABreak</a>:&nbsp;reference-free inversion discovery tool</li>
<li><a href="https://github.com/llecompte/SVJedi">SVJedi</a>: Structural Variant genotyper with long read data</li>
<li><a href="https://github.com/SandraLouise/SVJedi-graph">SVJedi-graph</a>: Structural Variant genotyper with long read data using a variation graph</li>
</ul><h2>Sequence assembly</h2><ul>
<li><a href="https://github.com/cguyomar/MinYS">MinYS</a>: reference-guided genome assembly in metagenomics data</li>
<li><a href="https://github.com/anne-gcd/MTG-Link">MTG-link</a>: local assembly tool for linked-read data</li>
<li><a href="https://gatb.inria.fr/software/minia/" title="Minia">Minia</a>: De novo short read assembler</li>
<li><a href="https://gatb.inria.fr/de-novo-genome-assembly/">de-novo pipeline</a>:&nbsp;<em>de-novo</em>&nbsp;assembly pipeline (error correction / contigs / scaffolding) for genomes and meta-genomes</li>
<li><a href="https://gatb.inria.fr/software/mapsembler/" title="Mapsembler2">Mapsembler2</a>: Targeted assembly (not maintained)</li>
</ul><h2>Managing k-mers &amp; indexation</h2><ul>
<li><a href="https://github.com/lrobidou/findere">findere</a>:&nbsp;simple strategy for speeding up queries and for reducing false positive calls from any Approximate Membership Query data structure.
<ul>
<li><a href="https://github.com/lrobidou/fimpera">fimpera</a>&nbsp;extends findere adding the abundance information.</li>
</ul>
</li>
<li><a href="https://github.com/tlemane/kmtricks">kmtricks</a>:&nbsp;modular tool suite for counting kmers, and constructing Bloom filters or kmer matrices, for large collections of sequencing data.</li>
<li><a href="https://github.com/tlemane/kmindex">kmindex&nbsp;</a>is a tool for indexing and querying sequencing samples. It is built on top of kmtricks.</li>
<li><a href="https://github.com/pierrepeterlongo/back_to_sequences">back to sequences</a>: Find sequences (reads, unitigs, genes) related to a set of kmers in large datasets, in a matter of seconds.</li>
<li><a href="https://github.com/vicLeva/bqf">Backpack Quotient Filter</a>:&nbsp;k-mer indexing data structure with abundance</li>
<li><a href="http://github.com/GATB/rconnector">short read connector</a>:&nbsp;Detect similar reads from potentially large read set</li>
<li><a href="https://gatb.inria.fr/software/dsk/" title="DSK">DSK</a>:&nbsp;Count K-mer in sequences</li>
</ul><h2>Pangenome graph manipulation</h2><ul>
<li><a href="https://github.com/Tharos-ux/pancat">Pancat</a>: Pangenome Comparison and Analysis Toolkit</li>
<li><a href="https://pypi.org/project/gfagraphs/">GFAGraphs</a>: a Python library to handle pangenome graph files in GFA format.</li>
</ul><h2>Comparative metagenomics with k-mers</h2><ul>
<li><a href="https://github.com/GATB/simka">Simka and SimkaMin</a>:&nbsp;Comparative metagenomics for large-scale datasets</li>
<li><a href="https://team.inria.fr/genscale/high-throughput-sequence-analysis/compreads-metagenomic-data-analysis/">Comparead &amp; Commet</a>:&nbsp;comparison of metagenomic datasets</li>
</ul><h2>Species and bacterial strains identification</h2><ul>
<li><a href="https://github.com/gsiekaniec/ORI">ORI</a>: software using long nanopore reads to identify bacteria present in a sample at the strain level</li>
<li><a href="https://github.com/kevsilva/StrainFLAIR">StrainFLAIR</a>:&nbsp;STRAIN-level proFiLing using vArIation gRaph</li>
</ul><h2>General-purpose sequencing data manipulation</h2><ul>
<li><a href="https://team.inria.fr/genscale/ngs-software/gassst/">GASSST</a>:&nbsp;long read mapper</li>
<li><a href="https://gatb.inria.fr/software/leon/" title="Leon">Leon</a>: short read compressor (now included in GATB-core)</li>
<li><a href="https://gatb.inria.fr/software/bloocoo/" title="Bloocoo">Bloocoo</a>:&nbsp;short read corrector</li>
<li><a href="https://github.com/GATB/bcalm">BCALM</a>:&nbsp;Construct compacted de Bruijn graphs (unitigs)</li>
</ul><h2>&nbsp;Protein Structure</h2><ul>
<li><a href="https://team.inria.fr/genscale/protein-structure/a-purva-contact-map-overlap-solver/">A_Purva</a>:&nbsp;Contact Map Overlap solver</li>
<li><a href="https://team.inria.fr/genscale/protein-structure/md-jeep-distance-geomtry-solver/">MD-Jeep</a>:&nbsp;Distance Geometry solver</li>
<li><a href="https://team.inria.fr/genscale/csa-comparative-structural-alignment/">CSA</a>:&nbsp;Comparative Structural Alignment</li>
</ul><h2>Workflow</h2><ul>
<li><a href="https://team.inria.fr/genscale/workflows/slicee/">SLICEE</a>:&nbsp;parallel execution of bioinformatics workflows</li>
</ul><h3>Comparative Genomics</h3><ul>
<li><a href="https://team.inria.fr/genscale/comparative-genomics/cassis/">CASSIS</a>:&nbsp;detection of rearrangement breakpoints</li>
<li><a href="https://team.inria.fr/genscale/high-throughput-sequence-analysis/plast-intensive-sequence-comparison/">PLAST</a>:&nbsp;intensive bank-to-bank sequence comparison</li>
<li><a href="https://github.com/stephanierobin/DrjBreakpointFinder">DRJBreakpointFinder</a>: detection and precise localization of excision sites in proviral segments</li>
</ul>]]></description>
	<dc:creator>LEGE</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21242/summer-intern-research-bioinformatics</guid>
  <pubDate>Mon, 16 Feb 2015 12:26:32 -0600</pubDate>
  <link></link>
  <title><![CDATA[Summer Intern - Research Bioinformatics]]></title>
  <description><![CDATA[
<p>Be proficient in LINUX, know perl or python, understand biology and Next Generation Sequencing.<br />The intern will port Agile Assay Design pipelines into Galaxy.<br />The intern will also learn to develope his/her own bioinformatics pipelines for PCR or NGS data analysis.</p>

<p>Who you are<br />You’re someone who wants to influence your own development. You’re looking for a company where you have the opportunity to pursue your interests across functions and geographies. Where a job title is not considered the final definition of who you are, but the starting point.</p>

<p>Qualifications:<br />Major: Bioinformatcis or biology major who is interested and wants to learn Biocomputing, At least 2 years of college.<br />Basic knowledge of LINUX and programming, e.g., perl, python, XML.</p>

<p>More at http://www.roche.com/careers/jobs/jobsearch/job.htm?id=E-00437679&amp;locale=en&amp;title=Summer%20Intern%20-%20Research%20Bioinformatics</p>
]]></description>
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