feed.xml

<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="3.6.3">Jekyll</generator><link href="https://usegalaxy-au.github.io/feed.xml" rel="self" type="application/atom+xml" /><link href="https://usegalaxy-au.github.io/" rel="alternate" type="text/html" /><updated>2022-03-25T04:26:36+00:00</updated><id>https://usegalaxy-au.github.io/feed.xml</id><title type="html">Galaxy Australia</title><subtitle>The Australian Galaxy Instance</subtitle><entry><title type="html">Galaxy Australia tool updates 2022-03-23</title><link href="https://usegalaxy-au.github.io/posts/2022/03/23/tool-updates/" rel="alternate" type="text/html" title="Galaxy Australia tool updates 2022-03-23" /><published>2022-03-23T00:00:00+00:00</published><updated>2022-03-23T00:00:00+00:00</updated><id>https://usegalaxy-au.github.io/posts/2022/03/23/tool-updates</id><content type="html" xml:base="https://usegalaxy-au.github.io/posts/2022/03/23/tool-updates/">&lt;style&gt;
  table {
    width: 100%;
    margin: 10px 20px;
  }
  table th {
    display: none;
  }
  td {
    padding: 3px 5px;
  }
  tr td:nth-child(1) {
    vertical-align: top;
    width: 25%;
  }
&lt;/style&gt;

&lt;h3 id=&quot;tools-installed&quot;&gt;Tools installed&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Phylogenetics&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;gblocks &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/earlhaminst/gblocks/daf61c79c8b4&quot;&gt;daf61c79c8b4&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;

&lt;h3 id=&quot;tools-updated&quot;&gt;Tools updated&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Annotation&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;tbprofiler &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/tbprofiler/ac8250086ac3&quot;&gt;ac8250086ac3&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Assembly&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;racon &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/racon/d865b62f501c&quot;&gt;d865b62f501c&lt;/a&gt;&lt;br /&gt;raven &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/raven/2b2a352488fa&quot;&gt;2b2a352488fa&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;ChemicalToolBox&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;gmx_merge_topology_files &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/chemteam/gmx_merge_topology_files/04abdf96978b&quot;&gt;04abdf96978b&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Phylogenetics&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;nextclade &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/nextclade/9e10ba792be2&quot;&gt;9e10ba792be2&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Picard&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;picard &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/devteam/picard/1aac2a13842a&quot;&gt;1aac2a13842a&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;RAD-seq&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;stacks_assembleperead &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_assembleperead/6eaf0f9836c8&quot;&gt;6eaf0f9836c8&lt;/a&gt;&lt;br /&gt;stacks_clonefilter &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_clonefilter/3009a21724e7&quot;&gt;3009a21724e7&lt;/a&gt;&lt;br /&gt;stacks_cstacks &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_cstacks/be3df81c0353&quot;&gt;be3df81c0353&lt;/a&gt;&lt;br /&gt;stacks_denovomap &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_denovomap/9f9d39f582f3&quot;&gt;9f9d39f582f3&lt;/a&gt;&lt;br /&gt;stacks_genotypes &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_genotypes/46f061f3cfeb&quot;&gt;46f061f3cfeb&lt;/a&gt;&lt;br /&gt;stacks_populations &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_populations/95286af4139b&quot;&gt;95286af4139b&lt;/a&gt;&lt;br /&gt;stacks_procrad &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_procrad/be78e39d56b3&quot;&gt;be78e39d56b3&lt;/a&gt;&lt;br /&gt;stacks_pstacks &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_pstacks/67cbd80b83f5&quot;&gt;67cbd80b83f5&lt;/a&gt;&lt;br /&gt;stacks_refmap &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_refmap/1ba1185929c1&quot;&gt;1ba1185929c1&lt;/a&gt;&lt;br /&gt;stacks_rxstacks &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_rxstacks/3e43e51b3c3b&quot;&gt;3e43e51b3c3b&lt;/a&gt;&lt;br /&gt;stacks_sstacks &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_sstacks/563af4497055&quot;&gt;563af4497055&lt;/a&gt;&lt;br /&gt;stacks_stats &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_stats/93b16407d6e9&quot;&gt;93b16407d6e9&lt;/a&gt;&lt;br /&gt;stacks_ustacks &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_ustacks/a4ec4f620a77&quot;&gt;a4ec4f620a77&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Variant Calling&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;tbvcfreport &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/tbvcfreport/4934c0ac6197&quot;&gt;4934c0ac6197&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;</content><author><name></name></author><category term="tools" /><summary type="html"></summary></entry><entry><title type="html">Galaxy Australia tool updates 2022-03-16</title><link href="https://usegalaxy-au.github.io/posts/2022/03/16/tool-updates/" rel="alternate" type="text/html" title="Galaxy Australia tool updates 2022-03-16" /><published>2022-03-16T00:00:00+00:00</published><updated>2022-03-16T00:00:00+00:00</updated><id>https://usegalaxy-au.github.io/posts/2022/03/16/tool-updates</id><content type="html" xml:base="https://usegalaxy-au.github.io/posts/2022/03/16/tool-updates/">&lt;style&gt;
  table {
    width: 100%;
    margin: 10px 20px;
  }
  table th {
    display: none;
  }
  td {
    padding: 3px 5px;
  }
  tr td:nth-child(1) {
    vertical-align: top;
    width: 25%;
  }
&lt;/style&gt;

&lt;h3 id=&quot;tools-installed&quot;&gt;Tools installed&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Annotation&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;repeatmodeler &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/csbl/repeatmodeler/41bfbaf3c959&quot;&gt;41bfbaf3c959&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;ChemicalToolBox&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;autodock_vina_prepare_box &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/autodock_vina_prepare_box/8f766d9652a2&quot;&gt;8f766d9652a2&lt;/a&gt;&lt;br /&gt;autodock_vina_prepare_receptor &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/autodock_vina_prepare_receptor/05a13d377b28&quot;&gt;05a13d377b28&lt;/a&gt;&lt;br /&gt;fpocket &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/fpocket/4cc9d85c3bae&quot;&gt;4cc9d85c3bae&lt;/a&gt;&lt;br /&gt;openbabel_svg_depiction &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/openbabel_svg_depiction/7672039a0bb0&quot;&gt;7672039a0bb0&lt;/a&gt;&lt;br /&gt;rxdock_rbcavity &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/rxdock_rbcavity/0848d3b1a46f&quot;&gt;0848d3b1a46f&lt;/a&gt;&lt;br /&gt;rxdock_rbdock &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/rxdock_rbdock/b34d068c2782&quot;&gt;b34d068c2782&lt;/a&gt;&lt;br /&gt;sdf_to_tab &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/sdf_to_tab/4beb3e026bbb&quot;&gt;4beb3e026bbb&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Metagenomic Analysis&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;humann2 &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/humann2/cda49fede0c2&quot;&gt;cda49fede0c2&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Single-cell&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;music_construct_eset &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_construct_eset/7ffaa0968da3&quot;&gt;7ffaa0968da3&lt;/a&gt;&lt;br /&gt;music_deconvolution &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_deconvolution/56371b5a2da9&quot;&gt;56371b5a2da9&lt;/a&gt;&lt;br /&gt;music_inspect_eset &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_inspect_eset/8c64a2da3869&quot;&gt;8c64a2da3869&lt;/a&gt;&lt;br /&gt;raceid_clustering &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/raceid_clustering/f911a64454fb&quot;&gt;f911a64454fb&lt;/a&gt;&lt;br /&gt;raceid_inspectclusters &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspectclusters/2b0d3e2f402a&quot;&gt;2b0d3e2f402a&lt;/a&gt;&lt;br /&gt;raceid_inspecttrajectory &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspecttrajectory/df8e4e54d367&quot;&gt;df8e4e54d367&lt;/a&gt;&lt;br /&gt;raceid_trajectory &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/raceid_trajectory/c92d0f9338c5&quot;&gt;c92d0f9338c5&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;

&lt;h3 id=&quot;tools-updated&quot;&gt;Tools updated&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;ChemicalToolBox&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;gmx_merge_topology_files &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/chemteam/gmx_merge_topology_files/930a403f7389&quot;&gt;930a403f7389&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;FASTA/FASTQ&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;fastq_paired_end_splitter &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_splitter/e39cc71d3ed6&quot;&gt;e39cc71d3ed6&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;VCF/BCF&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;bcftools_annotate &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_annotate/2958e3b49ad4&quot;&gt;2958e3b49ad4&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;</content><author><name></name></author><category term="tools" /><summary type="html"></summary></entry><entry><title type="html">Galaxy Australia tool updates 2022-03-08</title><link href="https://usegalaxy-au.github.io/posts/2022/03/08/tool-updates/" rel="alternate" type="text/html" title="Galaxy Australia tool updates 2022-03-08" /><published>2022-03-08T00:00:00+00:00</published><updated>2022-03-08T00:00:00+00:00</updated><id>https://usegalaxy-au.github.io/posts/2022/03/08/tool-updates</id><content type="html" xml:base="https://usegalaxy-au.github.io/posts/2022/03/08/tool-updates/">&lt;style&gt;
  table {
    width: 100%;
    margin: 10px 20px;
  }
  table th {
    display: none;
  }
  td {
    padding: 3px 5px;
  }
  tr td:nth-child(1) {
    vertical-align: top;
    width: 25%;
  }
&lt;/style&gt;

&lt;h3 id=&quot;tools-installed&quot;&gt;Tools installed&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Phylogenetics&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;nextclade &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/nextclade/daddf188c13f&quot;&gt;daddf188c13f&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;SAM/BAM&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;bamutil_diff &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bamutil_diff/c28c4c132459&quot;&gt;c28c4c132459&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;

&lt;h3 id=&quot;tools-updated&quot;&gt;Tools updated&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;FASTA/FASTQ&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;cutadapt &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt/c5e2e5902201&quot;&gt;c5e2e5902201&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Picard&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;picard &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/devteam/picard/881d7645d1bf&quot;&gt;881d7645d1bf&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;RNA-seq&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;limma_voom &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/limma_voom/d6f5fa4ee473&quot;&gt;d6f5fa4ee473&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Send Data&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;ena_upload &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ena_upload/6f6537780379&quot;&gt;6f6537780379&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Variant Calling&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;freebayes &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/devteam/freebayes/a7c9782130e8&quot;&gt;a7c9782130e8&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;</content><author><name></name></author><category term="tools" /><summary type="html"></summary></entry><entry><title type="html">Galaxy Australia tool updates 2022-03-01</title><link href="https://usegalaxy-au.github.io/posts/2022/03/01/tool-updates/" rel="alternate" type="text/html" title="Galaxy Australia tool updates 2022-03-01" /><published>2022-03-01T00:00:00+00:00</published><updated>2022-03-01T00:00:00+00:00</updated><id>https://usegalaxy-au.github.io/posts/2022/03/01/tool-updates</id><content type="html" xml:base="https://usegalaxy-au.github.io/posts/2022/03/01/tool-updates/">&lt;style&gt;
  table {
    width: 100%;
    margin: 10px 20px;
  }
  table th {
    display: none;
  }
  td {
    padding: 3px 5px;
  }
  tr td:nth-child(1) {
    vertical-align: top;
    width: 25%;
  }
&lt;/style&gt;

&lt;h3 id=&quot;tools-installed&quot;&gt;Tools installed&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Assembly&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;links &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/links/7acd9ade2dd1&quot;&gt;7acd9ade2dd1&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;

&lt;h3 id=&quot;tools-updated&quot;&gt;Tools updated&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Assembly&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;metaspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/metaspades/eb7a370f6588&quot;&gt;eb7a370f6588&lt;/a&gt;&lt;br /&gt;rnaspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/rnaspades/e122f9101584&quot;&gt;e122f9101584&lt;/a&gt;&lt;br /&gt;spades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/spades/dd7ad84f3943&quot;&gt;dd7ad84f3943&lt;/a&gt;&lt;br /&gt;spades_plasmidspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_plasmidspades/85fb02c43042&quot;&gt;85fb02c43042&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;FASTQ Quality Control&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;filtlong &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/filtlong/41b2ad601cf0&quot;&gt;41b2ad601cf0&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Imaging&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;overlay_segmentation_mask &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/imgteam/overlay_segmentation_mask/22e573b7dcb1&quot;&gt;22e573b7dcb1&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Nanopore&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;porechop &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/porechop/543cbeef3949&quot;&gt;543cbeef3949&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Proteomics&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;cardinal_classification &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/cardinal_classification/8337ff96a54b&quot;&gt;8337ff96a54b&lt;/a&gt;&lt;br /&gt;cardinal_combine &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/cardinal_combine/2b1868ab3724&quot;&gt;2b1868ab3724&lt;/a&gt;&lt;br /&gt;cardinal_data_exporter &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/cardinal_data_exporter/b6a4dd06cde0&quot;&gt;b6a4dd06cde0&lt;/a&gt;&lt;br /&gt;cardinal_filtering &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/cardinal_filtering/1990986966c1&quot;&gt;1990986966c1&lt;/a&gt;&lt;br /&gt;cardinal_mz_images &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/cardinal_mz_images/c4df3005e04d&quot;&gt;c4df3005e04d&lt;/a&gt;&lt;br /&gt;cardinal_preprocessing &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/cardinal_preprocessing/798da6bdff3d&quot;&gt;798da6bdff3d&lt;/a&gt;&lt;br /&gt;cardinal_quality_report &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/cardinal_quality_report/fde8ba3a0766&quot;&gt;fde8ba3a0766&lt;/a&gt;&lt;br /&gt;cardinal_segmentations &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/cardinal_segmentations/653ad2b367f2&quot;&gt;653ad2b367f2&lt;/a&gt;&lt;br /&gt;cardinal_spectra_plots &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/cardinal_spectra_plots/12dde78d554b&quot;&gt;12dde78d554b&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;VCF/BCF&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;bcftools_call &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_call/d267bcfdc8fe&quot;&gt;d267bcfdc8fe&lt;/a&gt;&lt;br /&gt;bcftools_cnv &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_cnv/8d637025a905&quot;&gt;8d637025a905&lt;/a&gt;&lt;br /&gt;bcftools_concat &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_concat/fc47ffec447e&quot;&gt;fc47ffec447e&lt;/a&gt;&lt;br /&gt;bcftools_consensus &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_consensus/edc3d484b99a&quot;&gt;edc3d484b99a&lt;/a&gt;&lt;br /&gt;bcftools_convert_from_vcf &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_from_vcf/34585fd4bd3e&quot;&gt;34585fd4bd3e&lt;/a&gt;&lt;br /&gt;bcftools_convert_to_vcf &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_to_vcf/41873b29860a&quot;&gt;41873b29860a&lt;/a&gt;&lt;br /&gt;bcftools_csq &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/68216882a410&quot;&gt;68216882a410&lt;/a&gt;&lt;br /&gt;bcftools_filter &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_filter/e4988fd4d503&quot;&gt;e4988fd4d503&lt;/a&gt;&lt;br /&gt;bcftools_gtcheck &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_gtcheck/64778f8899cc&quot;&gt;64778f8899cc&lt;/a&gt;&lt;br /&gt;bcftools_isec &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_isec/4afd849c9d35&quot;&gt;4afd849c9d35&lt;/a&gt;&lt;br /&gt;bcftools_merge &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_merge/798c063f8fc9&quot;&gt;798c063f8fc9&lt;/a&gt;&lt;br /&gt;bcftools_norm &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_norm/481476814acc&quot;&gt;481476814acc&lt;/a&gt;&lt;br /&gt;bcftools_plugin_counts &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_counts/8d5d8355559b&quot;&gt;8d5d8355559b&lt;/a&gt;&lt;br /&gt;bcftools_plugin_dosage &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_dosage/de1764eb139f&quot;&gt;de1764eb139f&lt;/a&gt;&lt;br /&gt;bcftools_plugin_fill_an_ac &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_fill_an_ac/ab8afa393997&quot;&gt;ab8afa393997&lt;/a&gt;&lt;br /&gt;bcftools_plugin_fill_tags &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_fill_tags/3828c11c88b0&quot;&gt;3828c11c88b0&lt;/a&gt;&lt;br /&gt;bcftools_plugin_fixploidy &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_fixploidy/068e100f634a&quot;&gt;068e100f634a&lt;/a&gt;&lt;br /&gt;bcftools_plugin_impute_info &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_impute_info/cb1d846a29b8&quot;&gt;cb1d846a29b8&lt;/a&gt;&lt;br /&gt;bcftools_plugin_mendelian &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_mendelian/32a039e689d6&quot;&gt;32a039e689d6&lt;/a&gt;&lt;br /&gt;bcftools_plugin_missing2ref &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_missing2ref/bbc9a1e89ca6&quot;&gt;bbc9a1e89ca6&lt;/a&gt;&lt;br /&gt;bcftools_plugin_setgt &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_setgt/99238dfb46cb&quot;&gt;99238dfb46cb&lt;/a&gt;&lt;br /&gt;bcftools_plugin_tag2tag &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_tag2tag/f35cc95efb32&quot;&gt;f35cc95efb32&lt;/a&gt;&lt;br /&gt;bcftools_query &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query/94c5f302f0ea&quot;&gt;94c5f302f0ea&lt;/a&gt;&lt;br /&gt;bcftools_query_list_samples &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query_list_samples/57c0f25c6fcb&quot;&gt;57c0f25c6fcb&lt;/a&gt;&lt;br /&gt;bcftools_reheader &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_reheader/6993b945aefc&quot;&gt;6993b945aefc&lt;/a&gt;&lt;br /&gt;bcftools_roh &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_roh/fb3af223ff33&quot;&gt;fb3af223ff33&lt;/a&gt;&lt;br /&gt;bcftools_stats &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_stats/80844da35ed5&quot;&gt;80844da35ed5&lt;/a&gt;&lt;br /&gt;bcftools_view &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_view/e1a2389af238&quot;&gt;e1a2389af238&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;</content><author><name></name></author><category term="tools" /><summary type="html"></summary></entry><entry><title type="html">Galaxy Australia tool updates 2022-02-22</title><link href="https://usegalaxy-au.github.io/posts/2022/02/22/tool-updates/" rel="alternate" type="text/html" title="Galaxy Australia tool updates 2022-02-22" /><published>2022-02-22T00:00:00+00:00</published><updated>2022-02-22T00:00:00+00:00</updated><id>https://usegalaxy-au.github.io/posts/2022/02/22/tool-updates</id><content type="html" xml:base="https://usegalaxy-au.github.io/posts/2022/02/22/tool-updates/">&lt;style&gt;
  table {
    width: 100%;
    margin: 10px 20px;
  }
  table th {
    display: none;
  }
  td {
    padding: 3px 5px;
  }
  tr td:nth-child(1) {
    vertical-align: top;
    width: 25%;
  }
&lt;/style&gt;

&lt;h3 id=&quot;tools-installed&quot;&gt;Tools installed&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Annotation&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;eggnog_mapper &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/eggnog_mapper/63662ae295d6&quot;&gt;63662ae295d6&lt;/a&gt;&lt;br /&gt;funannotate_annotate &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/funannotate_annotate/14f588312c56&quot;&gt;14f588312c56&lt;/a&gt;&lt;br /&gt;funannotate_compare &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/funannotate_compare/563a19373357&quot;&gt;563a19373357&lt;/a&gt;&lt;br /&gt;funannotate_predict &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/funannotate_predict/2bba2ff070d9&quot;&gt;2bba2ff070d9&lt;/a&gt;&lt;br /&gt;interproscan &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/interproscan/c55643c3d813&quot;&gt;c55643c3d813&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Nanopore&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;pycoqc &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pycoqc/3a2f2e24c37e&quot;&gt;3a2f2e24c37e&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;

&lt;h3 id=&quot;tools-updated&quot;&gt;Tools updated&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Assembly&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;metaspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/metaspades/e731ea24e48d&quot;&gt;e731ea24e48d&lt;/a&gt;&lt;br /&gt;quast &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/quast/875d0f36d66f&quot;&gt;875d0f36d66f&lt;/a&gt;&lt;br /&gt;rnaspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/rnaspades/53c2bc8c2ae3&quot;&gt;53c2bc8c2ae3&lt;/a&gt;&lt;br /&gt;spades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/spades/7897763d14ec&quot;&gt;7897763d14ec&lt;/a&gt;&lt;br /&gt;spades_plasmidspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_plasmidspades/340bc17f49cf&quot;&gt;340bc17f49cf&lt;/a&gt;&lt;br /&gt;spades_biosyntheticspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_biosyntheticspades/904bf932cf78&quot;&gt;904bf932cf78&lt;/a&gt;&lt;br /&gt;spades_coronaspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_coronaspades/0e02cc942d97&quot;&gt;0e02cc942d97&lt;/a&gt;&lt;br /&gt;spades_metaplasmidspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaplasmidspades/6b5a5842531e&quot;&gt;6b5a5842531e&lt;/a&gt;&lt;br /&gt;spades_metaviralspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaviralspades/9de69775f512&quot;&gt;9de69775f512&lt;/a&gt;&lt;br /&gt;spades_rnaviralspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_rnaviralspades/b65a43f70b99&quot;&gt;b65a43f70b99&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;DeepTools&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;deeptools_plot_correlation &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_correlation/e44978659400&quot;&gt;e44978659400&lt;/a&gt;&lt;br /&gt;deeptools_plot_heatmap &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_heatmap/42cb23d80271&quot;&gt;42cb23d80271&lt;/a&gt;&lt;br /&gt;deeptools_plot_pca &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_pca/7784523d9743&quot;&gt;7784523d9743&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;FASTA/FASTQ&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;fastp &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fastp/65b93b623c77&quot;&gt;65b93b623c77&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Imaging&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;2d_auto_threshold &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/imgteam/2d_auto_threshold/0c777d708acc&quot;&gt;0c777d708acc&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Metagenomic Analysis&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;metaphlan &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/metaphlan/a16313517e55&quot;&gt;a16313517e55&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;</content><author><name></name></author><category term="tools" /><summary type="html"></summary></entry><entry><title type="html">Galaxy Australia tool updates 2022-02-15</title><link href="https://usegalaxy-au.github.io/posts/2022/02/15/tool-updates/" rel="alternate" type="text/html" title="Galaxy Australia tool updates 2022-02-15" /><published>2022-02-15T00:00:00+00:00</published><updated>2022-02-15T00:00:00+00:00</updated><id>https://usegalaxy-au.github.io/posts/2022/02/15/tool-updates</id><content type="html" xml:base="https://usegalaxy-au.github.io/posts/2022/02/15/tool-updates/">&lt;style&gt;
  table {
    width: 100%;
    margin: 10px 20px;
  }
  table th {
    display: none;
  }
  td {
    padding: 3px 5px;
  }
  tr td:nth-child(1) {
    vertical-align: top;
    width: 25%;
  }
&lt;/style&gt;

&lt;h3 id=&quot;tools-installed&quot;&gt;Tools installed&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Annotation&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;aegean_canongff3 &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/aegean_canongff3/3f438bf5475d&quot;&gt;3f438bf5475d&lt;/a&gt;&lt;br /&gt;aegean_gaeval &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/aegean_gaeval/1dd7adc21b6d&quot;&gt;1dd7adc21b6d&lt;/a&gt;&lt;br /&gt;aegean_locuspocus &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/aegean_locuspocus/c4ac24510b55&quot;&gt;c4ac24510b55&lt;/a&gt;&lt;br /&gt;aegean_parseval &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/aegean_parseval/1b52f0c8ad7f&quot;&gt;1b52f0c8ad7f&lt;/a&gt;&lt;br /&gt;funannotate_clean &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/funannotate_clean/a230ea445788&quot;&gt;a230ea445788&lt;/a&gt;&lt;br /&gt;funannotate_sort &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/funannotate_sort/b3cf4684e9c7&quot;&gt;b3cf4684e9c7&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Metagenomic Analysis&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;metaphlan2 &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/metaphlan2/f60773e921fa&quot;&gt;f60773e921fa&lt;/a&gt;&lt;br /&gt;combine_metaphlan2_humann2 &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bebatut/combine_metaphlan2_humann2/e25efca0a49c&quot;&gt;e25efca0a49c&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;

&lt;h3 id=&quot;tools-updated&quot;&gt;Tools updated&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Annotation&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;maker &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/maker/a444254e9a57&quot;&gt;a444254e9a57&lt;/a&gt;&lt;br /&gt;maker_map_ids &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/maker_map_ids/e906fa778440&quot;&gt;e906fa778440&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Assembly&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;bionano_scaffold &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/bionano_scaffold/5258e18bbe23&quot;&gt;5258e18bbe23&lt;/a&gt;&lt;br /&gt;hifiasm &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hifiasm/5bec28269d95&quot;&gt;5bec28269d95&lt;/a&gt;&lt;br /&gt;megahit &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/megahit/14ddfc8ffb93&quot;&gt;14ddfc8ffb93&lt;/a&gt;&lt;br /&gt;spades_biosyntheticspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_biosyntheticspades/7490b213baa9&quot;&gt;7490b213baa9&lt;/a&gt;&lt;br /&gt;spades_coronaspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_coronaspades/d6e617c4e338&quot;&gt;d6e617c4e338&lt;/a&gt;&lt;br /&gt;spades_metaplasmidspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaplasmidspades/b8002c3f7141&quot;&gt;b8002c3f7141&lt;/a&gt;&lt;br /&gt;spades_metaviralspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaviralspades/2a10645aeadd&quot;&gt;2a10645aeadd&lt;/a&gt;&lt;br /&gt;spades_rnaviralspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_rnaviralspades/d159735a6a9f&quot;&gt;d159735a6a9f&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;DeepTools&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;deeptools_bam_compare &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_compare/c89b665b45e4&quot;&gt;c89b665b45e4&lt;/a&gt;&lt;br /&gt;deeptools_bam_coverage &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/4df95152a39e&quot;&gt;4df95152a39e&lt;/a&gt;&lt;br /&gt;deeptools_bam_pe_fragmentsize &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_pe_fragmentsize/3f9dc453c0e8&quot;&gt;3f9dc453c0e8&lt;/a&gt;&lt;br /&gt;deeptools_bigwig_compare &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bigwig_compare/7989c6ddf634&quot;&gt;7989c6ddf634&lt;/a&gt;&lt;br /&gt;deeptools_compute_gc_bias &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_compute_gc_bias/56d5b797ce84&quot;&gt;56d5b797ce84&lt;/a&gt;&lt;br /&gt;deeptools_compute_matrix &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_compute_matrix/19bb3e6d9e31&quot;&gt;19bb3e6d9e31&lt;/a&gt;&lt;br /&gt;deeptools_compute_matrix_operations &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_compute_matrix_operations/be95d48dd27f&quot;&gt;be95d48dd27f&lt;/a&gt;&lt;br /&gt;deeptools_correct_gc_bias &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_correct_gc_bias/00a71ff7c06b&quot;&gt;00a71ff7c06b&lt;/a&gt;&lt;br /&gt;deeptools_multi_bam_summary &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_multi_bam_summary/b4e53394fced&quot;&gt;b4e53394fced&lt;/a&gt;&lt;br /&gt;deeptools_multi_bigwig_summary &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_multi_bigwig_summary/459cfa861f0b&quot;&gt;459cfa861f0b&lt;/a&gt;&lt;br /&gt;deeptools_plot_coverage &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_coverage/7fda5607e777&quot;&gt;7fda5607e777&lt;/a&gt;&lt;br /&gt;deeptools_plot_enrichment &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_enrichment/88ce7fed1488&quot;&gt;88ce7fed1488&lt;/a&gt;&lt;br /&gt;deeptools_plot_fingerprint &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_fingerprint/ca8a7f0ea872&quot;&gt;ca8a7f0ea872&lt;/a&gt;&lt;br /&gt;deeptools_plot_profile &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_plot_profile/e9429e484e25&quot;&gt;e9429e484e25&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;FASTA/FASTQ&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;cutadapt &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt/48f587c13075&quot;&gt;48f587c13075&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Graph/Display Data&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;pygenometracks &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pygenometracks/a1abfa420d9d&quot;&gt;a1abfa420d9d&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Phylogenetics&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;pangolin &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pangolin/2fa9d4f1b48f&quot;&gt;2fa9d4f1b48f&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;</content><author><name></name></author><category term="tools" /><summary type="html"></summary></entry><entry><title type="html">Galaxy Australia tool updates 2022-02-08</title><link href="https://usegalaxy-au.github.io/posts/2022/02/08/tool-updates/" rel="alternate" type="text/html" title="Galaxy Australia tool updates 2022-02-08" /><published>2022-02-08T00:00:00+00:00</published><updated>2022-02-08T00:00:00+00:00</updated><id>https://usegalaxy-au.github.io/posts/2022/02/08/tool-updates</id><content type="html" xml:base="https://usegalaxy-au.github.io/posts/2022/02/08/tool-updates/">&lt;style&gt;
  table {
    width: 100%;
    margin: 10px 20px;
  }
  table th {
    display: none;
  }
  td {
    padding: 3px 5px;
  }
  tr td:nth-child(1) {
    vertical-align: top;
    width: 25%;
  }
&lt;/style&gt;

&lt;h3 id=&quot;tools-installed&quot;&gt;Tools installed&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Annotation&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;repeat_masker &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/repeat_masker/3f987772e283&quot;&gt;3f987772e283&lt;/a&gt;&lt;br /&gt;get_orfs_or_cdss &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/71905a6d52a7&quot;&gt;71905a6d52a7&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Assembly&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;masurca_simple &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/dnbenso/masurca_simple/0a33488ca043&quot;&gt;0a33488ca043&lt;/a&gt;&lt;br /&gt;minia &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/minia/734cd5f1c1b2&quot;&gt;734cd5f1c1b2&lt;/a&gt;&lt;br /&gt;spades_coronaspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_coronaspades/808b3a0a6716&quot;&gt;808b3a0a6716&lt;/a&gt;&lt;br /&gt;spades_metaplasmidspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaplasmidspades/8d4b90bf9caf&quot;&gt;8d4b90bf9caf&lt;/a&gt;&lt;br /&gt;spades_metaviralspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaviralspades/f1532cb33c75&quot;&gt;f1532cb33c75&lt;/a&gt;&lt;br /&gt;rnaspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/rnaspades/ef69617ecb42&quot;&gt;ef69617ecb42&lt;/a&gt;&lt;br /&gt;spades_plasmidspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_plasmidspades/e41dcb0e913b&quot;&gt;e41dcb0e913b&lt;/a&gt;&lt;br /&gt;spades_rnaviralspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spades_rnaviralspades/249f6a28c751&quot;&gt;249f6a28c751&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;

&lt;h3 id=&quot;tools-updated&quot;&gt;Tools updated&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Assembly&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;metaspades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/metaspades/f338e9942b27&quot;&gt;f338e9942b27&lt;/a&gt;&lt;br /&gt;spades &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/spades/d2d1df21dfb9&quot;&gt;d2d1df21dfb9&lt;/a&gt;&lt;br /&gt;pretext_map &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pretext_map/dfb8a4497339&quot;&gt;dfb8a4497339&lt;/a&gt;&lt;br /&gt;shovill &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/shovill/2a9baa0c4316&quot;&gt;2a9baa0c4316&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;BB Tools&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;bbtools_bbduk &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbduk/a9c9d768b751&quot;&gt;a9c9d768b751&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;FASTA/FASTQ&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;ucsc_fasplit &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ucsc_fasplit/bf04bd405d5b&quot;&gt;bf04bd405d5b&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;</content><author><name></name></author><category term="tools" /><summary type="html"></summary></entry><entry><title type="html">Galaxy Australia tool updates 2022-02-01</title><link href="https://usegalaxy-au.github.io/posts/2022/02/01/tool-updates/" rel="alternate" type="text/html" title="Galaxy Australia tool updates 2022-02-01" /><published>2022-02-01T00:00:00+00:00</published><updated>2022-02-01T00:00:00+00:00</updated><id>https://usegalaxy-au.github.io/posts/2022/02/01/tool-updates</id><content type="html" xml:base="https://usegalaxy-au.github.io/posts/2022/02/01/tool-updates/">&lt;style&gt;
  table {
    width: 100%;
    margin: 10px 20px;
  }
  table th {
    display: none;
  }
  td {
    padding: 3px 5px;
  }
  tr td:nth-child(1) {
    vertical-align: top;
    width: 25%;
  }
&lt;/style&gt;

&lt;h3 id=&quot;tools-updated&quot;&gt;Tools updated&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;ChemicalToolBox&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;ambertools_acpype &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/chemteam/ambertools_acpype/095ad4d096d1&quot;&gt;095ad4d096d1&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Mapping&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;bowtie2 &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/devteam/bowtie2/cd659e8cc5fa&quot;&gt;cd659e8cc5fa&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Phylogenetics&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;pangolin &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pangolin/5f8727ff21e7&quot;&gt;5f8727ff21e7&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;</content><author><name></name></author><category term="tools" /><summary type="html"></summary></entry><entry><title type="html">Galaxy Australia tool updates 2022-01-25</title><link href="https://usegalaxy-au.github.io/posts/2022/01/25/tool-updates/" rel="alternate" type="text/html" title="Galaxy Australia tool updates 2022-01-25" /><published>2022-01-25T00:00:00+00:00</published><updated>2022-01-25T00:00:00+00:00</updated><id>https://usegalaxy-au.github.io/posts/2022/01/25/tool-updates</id><content type="html" xml:base="https://usegalaxy-au.github.io/posts/2022/01/25/tool-updates/">&lt;style&gt;
  table {
    width: 100%;
    margin: 10px 20px;
  }
  table th {
    display: none;
  }
  td {
    padding: 3px 5px;
  }
  tr td:nth-child(1) {
    vertical-align: top;
    width: 25%;
  }
&lt;/style&gt;

&lt;h3 id=&quot;tools-updated&quot;&gt;Tools updated&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Assembly&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;abyss &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/abyss/8f1b150a2487&quot;&gt;8f1b150a2487&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Mapping&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;minimap2 &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/minimap2/11a0d50a54e6&quot;&gt;11a0d50a54e6&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;SAM/BAM&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;samtools_view &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/samtools_view/0dbf49c414ae&quot;&gt;0dbf49c414ae&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;</content><author><name></name></author><category term="tools" /><summary type="html"></summary></entry><entry><title type="html">Galaxy Australia tool updates 2022-01-18</title><link href="https://usegalaxy-au.github.io/posts/2022/01/18/tool-updates/" rel="alternate" type="text/html" title="Galaxy Australia tool updates 2022-01-18" /><published>2022-01-18T00:00:00+00:00</published><updated>2022-01-18T00:00:00+00:00</updated><id>https://usegalaxy-au.github.io/posts/2022/01/18/tool-updates</id><content type="html" xml:base="https://usegalaxy-au.github.io/posts/2022/01/18/tool-updates/">&lt;style&gt;
  table {
    width: 100%;
    margin: 10px 20px;
  }
  table th {
    display: none;
  }
  td {
    padding: 3px 5px;
  }
  tr td:nth-child(1) {
    vertical-align: top;
    width: 25%;
  }
&lt;/style&gt;

&lt;h3 id=&quot;tools-installed&quot;&gt;Tools installed&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Assembly&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;bionano_scaffold &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/bionano_scaffold/a7f16f24e9a1&quot;&gt;a7f16f24e9a1&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Proteomics&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;encyclopedia_searchtolib &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/encyclopedia_searchtolib/36880dfd9fa7&quot;&gt;36880dfd9fa7&lt;/a&gt;&lt;br /&gt;openms_targetedfileconverter &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_targetedfileconverter/dd71e020e2aa&quot;&gt;dd71e020e2aa&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Variant Calling&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;cutesv &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cutesv/c0f8fe52948e&quot;&gt;c0f8fe52948e&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;

&lt;h3 id=&quot;tools-updated&quot;&gt;Tools updated&lt;/h3&gt;

&lt;table&gt;
  &lt;thead&gt;
    &lt;tr&gt;
      &lt;th&gt;Section&lt;/th&gt;
      &lt;th&gt;Tool&lt;/th&gt;
    &lt;/tr&gt;
  &lt;/thead&gt;
  &lt;tbody&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Multiple Alignments&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;mafft &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/rnateam/mafft/f1a5908ea2cb&quot;&gt;f1a5908ea2cb&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
      &lt;td&gt;&lt;strong&gt;Phylogenetics&lt;/strong&gt;&lt;/td&gt;
      &lt;td&gt;pangolin &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pangolin/ca0d8cf80567&quot;&gt;ca0d8cf80567&lt;/a&gt;&lt;/td&gt;
    &lt;/tr&gt;
  &lt;/tbody&gt;
&lt;/table&gt;</content><author><name></name></author><category term="tools" /><summary type="html"></summary></entry></feed>