https://livesys.se/tags/next-generation-sequencing/ Recent content in Next-Generation Sequencing on Living Systems_ Hugo en-us Thu, 19 Feb 2015 20:44:00 +0100 https://livesys.se/posts/hadoop-ngs-workshop/ Thu, 19 Feb 2015 20:44:00 +0100 https://livesys.se/posts/hadoop-ngs-workshop/ <p>Some random links from the <a href="https://biobankcloud.com/?q=ngs-workshop" target="_blank" rel="noopener">Hadoop for Next-Gen Sequencing workshop</a> held at KTH in Kista, Stockholm in February 2015.</p> <ul> <li> <p><strong>UPDATE: <a href="http://www.biobankcloud.eu/?q=ngs-workshop-videos-slides" target="_blank" rel="noopener">Slides and Videos now available</a> !</strong></p> </li> <li> <p><a href="https://github.com/andypetrella/spark-notebook" target="_blank" rel="noopener">Spark notebook</a> </p> <ul> <li><a href="https://github.com/Bridgewater/scala-notebook" target="_blank" rel="noopener">Scala notebook</a> </li> </ul> </li> <li> <p><a href="https://amplab.cs.berkeley.edu/publication/adam-genomics-formats-and-processing-patterns-for-cloud-scale-computing/" target="_blank" rel="noopener">ADAM</a> </p> <ul> <li>By <a href="http://bdgenomics.org/" target="_blank" rel="noopener">Big Data Genomics</a> </li> </ul> </li> <li> <p><a href="https://twitter.com/fnothaft/status/568413764376256512" target="_blank" rel="noopener">Tweet by Frank Nothaft on common workflow def</a> </p> <ul> <li>Part of <a href="http://genomicsandhealth.org/our-work/working-groups/data-working-group" target="_blank" rel="noopener">Global Alliance for &hellip;</a> </li> <li>Another link is <a href="http://ga4gh.org/" target="_blank" rel="noopener">ga4gh.org</a> </li> </ul> </li> <li> <p><a href="http://tachyon-project.org/" target="_blank" rel="noopener">Tachyon</a> in-memory file system</p> </li> <li> <p><a href="https://github.com/samuell/cuneiform" target="_blank" rel="noopener">Cuneiform</a> </p> <ul> <li>Does support multiple outputs etc</li> <li>Black-box vs. White-box</li> <li>Workflow dependency graph can be dynamically built up while you&rsquo;re running</li> <li>Can specity tasks in any scripting languages, or in cuneiform itself</li> </ul> </li> <li> <p><a href="https://github.com/samuell/Hi-WAY" target="_blank" rel="noopener">Hi-Way</a> </p> https://livesys.se/posts/introductory-course-in-bioinformatics-for-ngs-data/ Mon, 09 Feb 2015 20:44:00 +0100 https://livesys.se/posts/introductory-course-in-bioinformatics-for-ngs-data/ <!-- raw HTML omitted --> <p>Right now I&rsquo;m sitting on the train and trying to get my head around some of the <a href="http://uppnex.se/twiki/do/view/Courses/NgsIntro1502/PrecourseMaterial" target="_blank" rel="noopener">pre-course materials</a> .</p>