Updates

rss.xml

@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?><rss xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:atom="http://www.w3.org/2005/Atom" version="2.0"><channel><title><![CDATA[EPI2ME Labs's RSS Feed]]></title><description><![CDATA[Tutorials and workflows for nanopore sequencing.]]></description><link>https://labs.epi2me.io</link><generator>GatsbyJS</generator><lastBuildDate>Wed, 11 Sep 2024 14:01:36 GMT</lastBuildDate><item><title><![CDATA[EPI2ME 24.08-01 Release]]></title><description><![CDATA[With the ever-growing popularity of EPI2ME workflows, we present a consolidated maintenance release of a selection of our workflows.]]></description><link>https://labs.epi2me.io/epi2me-24.08-01-release</link><guid isPermaLink="false">https://labs.epi2me.io/epi2me-24.08-01-release</guid><pubDate>Thu, 15 Aug 2024 00:00:00 GMT</pubDate><enclosure url="https://labs.epi2me.io/static/9e355e5d83546ee4854201a1b09aeba6/59ccf/red-panda.jpg" length="0" type="image/jpeg"/><content:encoded>&lt;p&gt;Dear Nanopore Community,&lt;/p&gt;&lt;p&gt;In this late summer release, we are pleased to introduce a collection of technical updates and improvements to our EPI2ME workflows.&lt;/p&gt;&lt;ul&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-clone-validation/releases/v1.4.0&quot;&gt;wf-clone-validation v1.4.0&lt;/a&gt; can now better accommodate multiplexed runs where expected plasmid sequence lengths vary considerably - an approximate size can now be specified for each plasmid within the sample sheet. &lt;ul&gt;&lt;li&gt;Emit assembly quality stats in supplementary TSV file (not just in HTML report)&lt;/li&gt;&lt;li&gt;Better basecall model handling - see the linked changelog&lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-pore-c/releases/v1.2.1&quot;&gt;wf-pore-c v1.2.1&lt;/a&gt; has been updated to more efficiently use available memory; the update also includes improvements to the handling of modified base tag information.&lt;ul&gt;&lt;li&gt;bed parameter now outputs the paired end BAM required for downstream tools&lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-human-variation/releases/v2.3.1&quot;&gt;wf-human-variation v2.3.1&lt;/a&gt; maintenance and fix release&lt;ul&gt;&lt;li&gt;Several bug fixes and stability improvements&lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-somatic-variation/releases/v1.3.1&quot;&gt;wf-somatic-variation v1.3.1&lt;/a&gt; maintenance and fix release&lt;ul&gt;&lt;li&gt;Bug fixes and stability improvements&lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-transcriptomes/releases/v1.3.0&quot;&gt;wf-transcriptomes v1.3.0&lt;/a&gt; &lt;ul&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/pychopper&quot;&gt;Pychopper v2.7.10&lt;/a&gt; has been updated to the latest version - this introduces workflow support for cDNA kits: PCS114, PCB111 and PCB114 &lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-single-cell/releases/v2.2.0&quot;&gt;wf-single-cell v2.2.0&lt;/a&gt; &lt;ul&gt;&lt;li&gt;The workflow report now includes an alignment summary table.&lt;/li&gt;&lt;li&gt;10x visium (v1) support added.&lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-aav-qc/releases/tag/v1.1.1&quot;&gt;wf-aav-qc v1.1.1&lt;/a&gt;     &lt;ul&gt;&lt;li&gt;Small bug fix to address missing report &lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;/ul&gt;&lt;p&gt;We look forwards to any feedback and welcome suggestions and requests for new workflows and functionality. We would also love to hear about any EPI2ME-compatible workflows that you have developed - do review the following community workflows:&lt;/p&gt;&lt;ul&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/GenomiqueENS/wf-toulligqc&quot;&gt;wf-toulligqc v1.3&lt;/a&gt; is a version of the ToulligQC software for review of sequencing run characteristics.&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/treangenlab/emu&quot;&gt;wf-emu&lt;/a&gt; provides an EPI2ME compatible nextflow implementation of the EMU software for relative abundance estimation of 16S rRNA sequences.&lt;/li&gt;&lt;/ul&gt;</content:encoded><content:thumbnail>https://labs.epi2me.io/static/9e355e5d83546ee4854201a1b09aeba6/59ccf/red-panda.jpg</content:thumbnail><content:toenail>https://labs.epi2me.io/static/9e355e5d83546ee4854201a1b09aeba6/red-panda.jpeg</content:toenail></item><item><title><![CDATA[Unexpected results, so now what?]]></title><description><![CDATA[Essentials of a Bioinformatician's toolkit.]]></description><link>https://labs.epi2me.io/post-meta-analysis</link><guid isPermaLink="false">https://labs.epi2me.io/post-meta-analysis</guid><pubDate>Tue, 02 Jul 2024 00:00:00 GMT</pubDate><enclosure url="https://labs.epi2me.io/static/dbffcedee84f530889e4d24dc0595ddc/59ccf/spider.jpg" length="0" type="image/jpeg"/><content:encoded>&lt;p&gt;You just finished the lab work for the experiment that will save the future of humankind.
+<?xml version="1.0" encoding="UTF-8"?><rss xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:atom="http://www.w3.org/2005/Atom" version="2.0"><channel><title><![CDATA[EPI2ME Labs's RSS Feed]]></title><description><![CDATA[Tutorials and workflows for nanopore sequencing.]]></description><link>https://labs.epi2me.io</link><generator>GatsbyJS</generator><lastBuildDate>Wed, 11 Sep 2024 14:07:57 GMT</lastBuildDate><item><title><![CDATA[EPI2ME 24.08-01 Release]]></title><description><![CDATA[With the ever-growing popularity of EPI2ME workflows, we present a consolidated maintenance release of a selection of our workflows.]]></description><link>https://labs.epi2me.io/epi2me-24.08-01-release</link><guid isPermaLink="false">https://labs.epi2me.io/epi2me-24.08-01-release</guid><pubDate>Thu, 15 Aug 2024 00:00:00 GMT</pubDate><enclosure url="https://labs.epi2me.io/static/9e355e5d83546ee4854201a1b09aeba6/59ccf/red-panda.jpg" length="0" type="image/jpeg"/><content:encoded>&lt;p&gt;Dear Nanopore Community,&lt;/p&gt;&lt;p&gt;In this late summer release, we are pleased to introduce a collection of technical updates and improvements to our EPI2ME workflows.&lt;/p&gt;&lt;ul&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-clone-validation/releases/v1.4.0&quot;&gt;wf-clone-validation v1.4.0&lt;/a&gt; can now better accommodate multiplexed runs where expected plasmid sequence lengths vary considerably - an approximate size can now be specified for each plasmid within the sample sheet. &lt;ul&gt;&lt;li&gt;Emit assembly quality stats in supplementary TSV file (not just in HTML report)&lt;/li&gt;&lt;li&gt;Better basecall model handling - see the linked changelog&lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-pore-c/releases/v1.2.1&quot;&gt;wf-pore-c v1.2.1&lt;/a&gt; has been updated to more efficiently use available memory; the update also includes improvements to the handling of modified base tag information.&lt;ul&gt;&lt;li&gt;bed parameter now outputs the paired end BAM required for downstream tools&lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-human-variation/releases/v2.3.1&quot;&gt;wf-human-variation v2.3.1&lt;/a&gt; maintenance and fix release&lt;ul&gt;&lt;li&gt;Several bug fixes and stability improvements&lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-somatic-variation/releases/v1.3.1&quot;&gt;wf-somatic-variation v1.3.1&lt;/a&gt; maintenance and fix release&lt;ul&gt;&lt;li&gt;Bug fixes and stability improvements&lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-transcriptomes/releases/v1.3.0&quot;&gt;wf-transcriptomes v1.3.0&lt;/a&gt; &lt;ul&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/pychopper&quot;&gt;Pychopper v2.7.10&lt;/a&gt; has been updated to the latest version - this introduces workflow support for cDNA kits: PCS114, PCB111 and PCB114 &lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-single-cell/releases/v2.2.0&quot;&gt;wf-single-cell v2.2.0&lt;/a&gt; &lt;ul&gt;&lt;li&gt;The workflow report now includes an alignment summary table.&lt;/li&gt;&lt;li&gt;10x visium (v1) support added.&lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/epi2me-labs/wf-aav-qc/releases/tag/v1.1.1&quot;&gt;wf-aav-qc v1.1.1&lt;/a&gt;     &lt;ul&gt;&lt;li&gt;Small bug fix to address missing report &lt;/li&gt;&lt;/ul&gt;&lt;/li&gt;&lt;/ul&gt;&lt;p&gt;We look forwards to any feedback and welcome suggestions and requests for new workflows and functionality. We would also love to hear about any EPI2ME-compatible workflows that you have developed - do review the following community workflows:&lt;/p&gt;&lt;ul&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/GenomiqueENS/wf-toulligqc&quot;&gt;wf-toulligqc v1.3&lt;/a&gt; is a version of the ToulligQC software for review of sequencing run characteristics.&lt;/li&gt;&lt;li&gt;&lt;a href=&quot;https://github.com/treangenlab/emu&quot;&gt;wf-emu&lt;/a&gt; provides an EPI2ME compatible nextflow implementation of the EMU software for relative abundance estimation of 16S rRNA sequences.&lt;/li&gt;&lt;/ul&gt;</content:encoded><content:thumbnail>https://labs.epi2me.io/static/9e355e5d83546ee4854201a1b09aeba6/59ccf/red-panda.jpg</content:thumbnail><content:toenail>https://labs.epi2me.io/static/9e355e5d83546ee4854201a1b09aeba6/red-panda.jpeg</content:toenail></item><item><title><![CDATA[Unexpected results, so now what?]]></title><description><![CDATA[Essentials of a Bioinformatician's toolkit.]]></description><link>https://labs.epi2me.io/post-meta-analysis</link><guid isPermaLink="false">https://labs.epi2me.io/post-meta-analysis</guid><pubDate>Tue, 02 Jul 2024 00:00:00 GMT</pubDate><enclosure url="https://labs.epi2me.io/static/dbffcedee84f530889e4d24dc0595ddc/59ccf/spider.jpg" length="0" type="image/jpeg"/><content:encoded>&lt;p&gt;You just finished the lab work for the experiment that will save the future of humankind.
 A huge amount of data is waiting to be interpreted; so you run wf-metagenomics to find out the taxonomic composition of your sample and… surprise!
 You get many unclassified or totally unexpected taxa! How is this possible? What should you do next?
 Well, do not panic!