<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/39903?offset=490</link>
	<atom:link href="https://bioinformaticsonline.com/related/39903?offset=490" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32190/dbg2olcefficient-assembly-of-large-genomes-using-long-erroneous-reads-of-the-third-generation-sequencing-technologies</guid>
	<pubDate>Wed, 19 Apr 2017 10:09:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32190/dbg2olcefficient-assembly-of-large-genomes-using-long-erroneous-reads-of-the-third-generation-sequencing-technologies</link>
	<title><![CDATA[DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies]]></title>
	<description><![CDATA[<p>DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies</p>
<p>Our work is published in Scientific Reports:</p>
<p>Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci. Rep. 6, 31900; doi: 10.1038/srep31900 (2016).</p>
<p><a href="http://www.nature.com/articles/srep31900">http://www.nature.com/articles/srep31900</a></p>
<p>The manual can be downloaded from:</p>
<p><a href="https://github.com/yechengxi/DBG2OLC/raw/master/Manual.docx">https://github.com/yechengxi/DBG2OLC/raw/master/Manual.docx</a></p>
<p>To use precompiled versions,please go to:</p>
<p><a href="https://github.com/yechengxi/DBG2OLC/tree/master/compiled">https://github.com/yechengxi/DBG2OLC/tree/master/compiled</a></p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="https://github.com/yechengxi/DBG2OLC" rel="nofollow">https://github.com/yechengxi/DBG2OLC</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/32719/download-assemblies-from-ncbi</guid>
	<pubDate>Mon, 15 May 2017 06:02:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/32719/download-assemblies-from-ncbi</link>
	<title><![CDATA[Download assemblies from NCBI]]></title>
	<description><![CDATA[<p>A new &ldquo;Download assemblies&rdquo; button is now available in the&nbsp;<a href="https://www.ncbi.nlm.nih.gov/assembly" target="_blank">Assembly</a>&nbsp;database. This makes it easy to download data for multiple genomes without having to write scripts.</p><p>For example, you can run a search in Assembly and use check boxes (see left side of screenshot below) to refine the set of genome assemblies of interest. Then, just open the &ldquo;Download assemblies&rdquo; menu, choose the source database (<a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank">GenBank</a>&nbsp;or&nbsp;<a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank">RefSeq</a>), choose the file type, and start the download. An archive file will be saved to your computer that can be expanded into a folder containing your selected genome data files.</p><p><img src="https://ncbiinsights.files.wordpress.com/2017/05/download_button.jpg?w=584" alt="image" width="584" height="444" style="border: 0px; border: 0px;"></p><p>&nbsp;</p><p>More at&nbsp;https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/08/genome-data-download-made-easy/</p>]]></description>
	<dc:creator>Bulbul</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33221/genome-annotation-transfer-utility-gatu</guid>
	<pubDate>Mon, 29 May 2017 05:54:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33221/genome-annotation-transfer-utility-gatu</link>
	<title><![CDATA[Genome Annotation Transfer Utility (GATU)]]></title>
	<description><![CDATA[<p>Genome Annotation Transfer Utility (GATU) was designed to facilitate quick, efficient annotation of similar genomes using genomes that have already been annotated. For example, whenever a new strain of SARS coronavirus is sequenced, it is possible, using GATU, to automatically annotate the new strain using a previously-annotated strain of SARS CoV. This saves researchers from tedious manual annotation of these sequences.</p>
<p>The program utilizes tBLASTn and BLASTn algorithms to map genes from the reference genome (the annotated strain) to the new sequence (the unannotated strain). The goal is to annotate the majority of the new genome&rsquo;s genes in a single step. ORFs present in the target genome and absent from the reference genome are also identified; these ORFs can be further analyzed using BLAST, VGO and BBB. Afterwards, they can either be accepted for/rejected from annotation. GATU can handle multiple-exon genes as well as mature peptides. Although it was designed for use with viral genomes, GATU can also be used to help annotate larger genomes (ie. bacterial genomes).</p>
<p>The output is saved in GenBank, XML, or EMBL file format.</p><p>Address of the bookmark: <a href="https://virology.uvic.ca/help/tool-help/help-books/genome-annotation-transfer-utility-gatu-documentation/" rel="nofollow">https://virology.uvic.ca/help/tool-help/help-books/genome-annotation-transfer-utility-gatu-documentation/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/35125/eugene-v-koonin-lab</guid>
  <pubDate>Tue, 09 Jan 2018 05:01:15 -0600</pubDate>
  <link></link>
  <title><![CDATA[Eugene V. Koonin Lab]]></title>
  <description><![CDATA[
<p>Interested in understanding the evolution of life. To obtain glimpses of such understanding, we employ existing and new methods of computational biology to perform research in several major areas.</p>

<p>https://www.ncbi.nlm.nih.gov/research/groups/koonin/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35823/regen-ancestral-genome-reconstruction-for-bacteria</guid>
	<pubDate>Tue, 06 Mar 2018 05:02:36 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35823/regen-ancestral-genome-reconstruction-for-bacteria</link>
	<title><![CDATA[REGEN: Ancestral Genome Reconstruction for Bacteria]]></title>
	<description><![CDATA[<p><span>REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order.&nbsp;</span></p><p>Address of the bookmark: <a href="http://www.mdpi.com/2073-4425/3/3/423" rel="nofollow">http://www.mdpi.com/2073-4425/3/3/423</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/36525/installing-bandage-on-ubunty</guid>
	<pubDate>Tue, 08 May 2018 08:03:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/36525/installing-bandage-on-ubunty</link>
	<title><![CDATA[Installing Bandage on Ubunty !]]></title>
	<description><![CDATA[<p>The following instructions successfully build Bandage (https://github.com/rrwick/Bandage ) on a fresh installation of Ubuntu 14.04:</p><ol>
<li>Ensure the package lists are up-to-date:&nbsp;<code>sudo apt-get update</code></li>
<li>Install prerequisite packages:&nbsp;<code>sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev</code></li>
<li>Download the Bandage code from GitHub:&nbsp;<code>git clone https://github.com/rrwick/Bandage.git</code></li>
<li>Open a terminal in the Bandage directory.</li>
<li>Set the environment variable to specify that you will be using Qt 5, not Qt 4:&nbsp;<code>export QT_SELECT=5</code></li>
<li>Run qmake to generate a Makefile:&nbsp;<code>qmake</code></li>
<li>Build the program:&nbsp;<code>make</code></li>
<li><code>Bandage</code>&nbsp;should now be an executable file.</li>
<li>Optionally, copy the program into /usr/local/bin:&nbsp;<code>sudo make install</code>. The Bandage build directory can then be deleted.</li>
</ol><p>➜ Tools git:(master) ✗ sudo apt-get update<br />[sudo] password for urbe:&nbsp;<br />Hit:1 http://ppa.launchpad.net/webupd8team/atom/ubuntu xenial InRelease<br />Get:2 http://security.ubuntu.com/ubuntu xenial-security InRelease [107 kB]&nbsp;<br />Hit:3 http://ppa.launchpad.net/webupd8team/java/ubuntu xenial InRelease&nbsp;<br />Hit:4 http://be.archive.ubuntu.com/ubuntu xenial InRelease&nbsp;<br />Get:5 http://be.archive.ubuntu.com/ubuntu xenial-updates InRelease [109 kB]<br />Get:6 http://be.archive.ubuntu.com/ubuntu xenial-backports InRelease [107 kB]&nbsp;<br />Get:7 https://cran.rstudio.com/bin/linux/ubuntu xenial/ InRelease [3.590 B]&nbsp;<br />Hit:8 https://download.docker.com/linux/ubuntu xenial InRelease&nbsp;<br />Ign:9 http://download.opensuse.org/repositories/home:/sionescu/Debian ./ InRelease&nbsp;<br />Hit:10 http://download.opensuse.org/repositories/home:/sionescu/Debian ./ Release&nbsp;<br />Get:11 http://packages.cloud.google.com/apt cloud-sdk-xenial InRelease [6.372 B]<br />Get:12 http://security.ubuntu.com/ubuntu xenial-security/main amd64 Packages [484 kB]<br />Get:13 http://security.ubuntu.com/ubuntu xenial-security/main i386 Packages [433 kB]<br />Get:14 http://security.ubuntu.com/ubuntu xenial-security/main Translation-en [209 kB]<br />Get:15 http://security.ubuntu.com/ubuntu xenial-security/main amd64 DEP-11 Metadata [67,5 kB]<br />Get:16 http://security.ubuntu.com/ubuntu xenial-security/main DEP-11 64x64 Icons [68,0 kB]&nbsp;<br />Get:17 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 DEP-11 Metadata [107 kB]<br />Get:18 http://security.ubuntu.com/ubuntu xenial-security/universe DEP-11 64x64 Icons [147 kB]<br />Get:19 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages [769 kB]&nbsp;<br />Get:20 http://be.archive.ubuntu.com/ubuntu xenial-updates/main i386 Packages [710 kB]&nbsp;<br />Get:21 http://be.archive.ubuntu.com/ubuntu xenial-updates/main Translation-en [319 kB]<br />Get:22 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 DEP-11 Metadata [319 kB]<br />Get:24 http://be.archive.ubuntu.com/ubuntu xenial-updates/main DEP-11 64x64 Icons [228 kB]&nbsp;<br />Get:25 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 DEP-11 Metadata [246 kB]<br />Err:11 http://packages.cloud.google.com/apt cloud-sdk-xenial InRelease&nbsp;<br />The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A030B21BA07F4FB<br />Get:26 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe DEP-11 64x64 Icons [331 kB]<br />Get:27 http://be.archive.ubuntu.com/ubuntu xenial-updates/multiverse amd64 DEP-11 Metadata [5.964 B]<br />Get:28 http://be.archive.ubuntu.com/ubuntu xenial-backports/main amd64 DEP-11 Metadata [3.328 B]<br />Get:29 http://be.archive.ubuntu.com/ubuntu xenial-backports/universe amd64 DEP-11 Metadata [5.088 B]<br />Fetched 4.779 kB in 2s (1.606 kB/s)&nbsp;<br />Reading package lists... Done<br />W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://packages.cloud.google.com/apt cloud-sdk-xenial InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A030B21BA07F4FB<br />W: Failed to fetch http://packages.cloud.google.com/apt/dists/cloud-sdk-xenial/InRelease The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A030B21BA07F4FB<br />W: Some index files failed to download. They have been ignored, or old ones used instead.<br />➜ Tools git:(master) ✗ sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev<br />Reading package lists... Done<br />Building dependency tree&nbsp;<br />Reading state information... Done<br />build-essential is already the newest version (12.1ubuntu2).<br />git is already the newest version (1:2.7.4-0ubuntu1.3).<br />The following packages were automatically installed and are no longer required:<br />bridge-utils containerd linux-headers-4.4.0-116 linux-headers-4.4.0-116-generic linux-headers-4.4.0-21 linux-headers-4.4.0-21-generic linux-image-4.4.0-116-generic linux-image-4.4.0-21-generic<br />linux-image-extra-4.4.0-116-generic linux-image-extra-4.4.0-21-generic linux-signed-image-4.4.0-116-generic runc ubuntu-fan<br />Use 'sudo apt autoremove' to remove them.<br />The following additional packages will be installed:<br />libdrm-dev libegl1-mesa-dev libgl1-mesa-dev libgles2-mesa libgles2-mesa-dev libglu1-mesa-dev libmirclient-dev libmircommon-dev libmircookie-dev libmircookie2 libmircore-dev libprotobuf-dev libprotobuf9v5<br />libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5printsupport5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5test5 libqt5widgets5 libqt5xml5 libwayland-bin<br />libwayland-dev libx11-xcb-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-randr0 libxcb-randr0-dev libxcb-render-util0 libxcb-render0-dev<br />libxcb-shape0-dev libxcb-sync-dev libxcb-xfixes0-dev libxcb-xkb1 libxdamage-dev libxext-dev libxfixes-dev libxkbcommon-dev libxkbcommon-x11-0 libxshmfence-dev libxxf86vm-dev mesa-common-dev qt5-qmake<br />qtbase5-dev-tools qttranslations5-l10n x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-xext-dev x11proto-xf86vidmode-dev<br />Suggested packages:<br />libqt5libqgtk2 qt5-image-formats-plugins qtwayland5 libxext-doc libmysqlclient-dev libpq-dev libsqlite3-dev unixodbc-dev<br />The following NEW packages will be installed:<br />libdrm-dev libegl1-mesa-dev libgl1-mesa-dev libgles2-mesa libgles2-mesa-dev libglu1-mesa-dev libmirclient-dev libmircommon-dev libmircookie-dev libmircookie2 libmircore-dev libprotobuf-dev libprotobuf9v5<br />libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5printsupport5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5svg5-dev libqt5test5 libqt5widgets5 libqt5xml5<br />libwayland-bin libwayland-dev libx11-xcb-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-randr0 libxcb-randr0-dev libxcb-render-util0<br />libxcb-render0-dev libxcb-shape0-dev libxcb-sync-dev libxcb-xfixes0-dev libxcb-xkb1 libxdamage-dev libxext-dev libxfixes-dev libxkbcommon-dev libxkbcommon-x11-0 libxshmfence-dev libxxf86vm-dev mesa-common-dev<br />qt5-qmake qtbase5-dev qtbase5-dev-tools qttranslations5-l10n x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-xext-dev x11proto-xf86vidmode-dev<br />0 upgraded, 64 newly installed, 0 to remove and 11 not upgraded.<br />Need to get 15,2 MB of archives.<br />After this operation, 78,5 MB of additional disk space will be used.<br />Do you want to continue? [Y/n] Y<br />Get:1 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5core5a amd64 5.5.1+dfsg-16ubuntu7.5 [1.817 kB]<br />Get:2 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5dbus5 amd64 5.5.1+dfsg-16ubuntu7.5 [175 kB]<br />Get:3 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5network5 amd64 5.5.1+dfsg-16ubuntu7.5 [540 kB]<br />Get:4 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-icccm4 amd64 0.4.1-1ubuntu1 [10,4 kB]<br />Get:5 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-image0 amd64 0.4.0-1build1 [12,3 kB]<br />Get:6 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-keysyms1 amd64 0.4.0-1 [8.406 B]<br />Get:7 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-randr0 amd64 1.11.1-1ubuntu1 [14,4 kB]<br />Get:8 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-render-util0 amd64 0.3.9-1 [9.638 B]<br />Get:9 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-xkb1 amd64 1.11.1-1ubuntu1 [29,2 kB]<br />Get:10 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxkbcommon-x11-0 amd64 0.5.0-1ubuntu2 [13,5 kB]<br />Get:11 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5gui5 amd64 5.5.1+dfsg-16ubuntu7.5 [2.290 kB]<br />Get:12 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5widgets5 amd64 5.5.1+dfsg-16ubuntu7.5 [2.252 kB]<br />Get:13 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libqt5svg5 amd64 5.5.1-2build1 [128 kB]<br />Get:14 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libqt5svg5-dev amd64 5.5.1-2build1 [9.724 B]<br />Get:15 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libdrm-dev amd64 2.4.83-1~16.04.1 [229 kB]<br />Get:16 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-dri2-dev all 2.8-2 [12,6 kB]<br />Get:17 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-gl-dev all 1.4.17-1 [17,9 kB]<br />Get:18 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-xext-dev all 7.3.0-1 [212 kB]<br />Get:19 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxext-dev amd64 2:1.3.3-1 [82,1 kB]<br />Get:20 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-xf86vidmode-dev all 2.3.1-2 [6.116 B]<br />Get:21 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxxf86vm-dev amd64 1:1.1.4-1 [13,3 kB]<br />Get:22 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-fixes-dev all 1:5.0-2ubuntu2 [14,2 kB]<br />Get:23 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxfixes-dev amd64 1:5.0.1-2 [10,9 kB]<br />Get:24 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-damage-dev all 1:1.2.1-2 [8.286 B]<br />Get:25 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxdamage-dev amd64 1:1.1.4-2 [5.028 B]<br />Get:26 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-glx0-dev amd64 1.11.1-1ubuntu1 [26,9 kB]<br />Get:27 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-dri2-0-dev amd64 1.11.1-1ubuntu1 [8.384 B]<br />Get:28 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-dri3-dev amd64 1.11.1-1ubuntu1 [5.752 B]<br />Get:29 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-render0-dev amd64 1.11.1-1ubuntu1 [15,3 kB]<br />Get:30 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-randr0-dev amd64 1.11.1-1ubuntu1 [18,2 kB]<br />Get:31 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-shape0-dev amd64 1.11.1-1ubuntu1 [6.900 B]<br />Get:32 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-xfixes0-dev amd64 1.11.1-1ubuntu1 [11,2 kB]<br />Get:33 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-sync-dev amd64 1.11.1-1ubuntu1 [10,1 kB]<br />Get:34 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-present-dev amd64 1.11.1-1ubuntu1 [6.618 B]<br />Get:35 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxshmfence-dev amd64 1.2-1 [3.676 B]<br />Get:36 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libx11-xcb-dev amd64 2:1.6.3-1ubuntu2 [9.730 B]<br />Get:37 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libwayland-bin amd64 1.12.0-1~ubuntu16.04.3 [18,4 kB]<br />Get:38 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libwayland-dev amd64 1.12.0-1~ubuntu16.04.3 [92,4 kB]<br />Get:39 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircore-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [23,7 kB]<br />Get:40 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libprotobuf9v5 amd64 2.6.1-1.3 [326 kB]<br />Get:41 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libprotobuf-dev amd64 2.6.1-1.3 [473 kB]<br />Get:42 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxkbcommon-dev amd64 0.5.0-1ubuntu2 [231 kB]<br />Get:43 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircommon-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [14,9 kB]<br />Get:44 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircookie2 amd64 0.26.3+16.04.20170605-0ubuntu1.1 [22,5 kB]<br />Get:45 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircookie-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [5.152 B]<br />Get:46 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmirclient-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [42,6 kB]<br />Get:47 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libegl1-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [19,9 kB]<br />Get:48 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgles2-mesa amd64 17.2.8-0ubuntu0~16.04.1 [13,4 kB]<br />Get:49 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgles2-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [40,2 kB]<br />Get:50 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 mesa-common-dev amd64 17.2.8-0ubuntu0~16.04.1 [525 kB]<br />Get:51 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgl1-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [4.456 B]<br />Get:52 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libglu1-mesa-dev amd64 9.0.0-2.1 [202 kB]<br />Get:53 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5concurrent5 amd64 5.5.1+dfsg-16ubuntu7.5 [24,3 kB]<br />Get:54 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5opengl5 amd64 5.5.1+dfsg-16ubuntu7.5 [128 kB]<br />Get:55 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5printsupport5 amd64 5.5.1+dfsg-16ubuntu7.5 [174 kB]<br />Get:56 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5sql5 amd64 5.5.1+dfsg-16ubuntu7.5 [104 kB]<br />Get:57 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5test5 amd64 5.5.1+dfsg-16ubuntu7.5 [84,5 kB]<br />Get:58 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5xml5 amd64 5.5.1+dfsg-16ubuntu7.5 [91,8 kB]<br />Get:59 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qt5-qmake amd64 5.5.1+dfsg-16ubuntu7.5 [1.192 kB]<br />Get:60 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qtbase5-dev-tools amd64 5.5.1+dfsg-16ubuntu7.5 [1.056 kB]<br />Get:61 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qtbase5-dev amd64 5.5.1+dfsg-16ubuntu7.5 [931 kB]<br />Get:62 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5opengl5-dev amd64 5.5.1+dfsg-16ubuntu7.5 [31,5 kB]<br />Get:63 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5sql5-sqlite amd64 5.5.1+dfsg-16ubuntu7.5 [33,0 kB]<br />Get:64 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 qttranslations5-l10n all 5.5.1-2build1 [1.210 kB]<br />Fetched 15,2 MB in 4s (3.099 kB/s)&nbsp;<br />Extracting templates from packages: 100%<br />Selecting previously unselected package libqt5core5a:amd64.<br />(Reading database ... 480949 files and directories currently installed.)<br />Preparing to unpack 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up libqt5svg5-dev:amd64 (5.5.1-2build1) ...<br />Setting up libdrm-dev:amd64 (2.4.83-1~16.04.1) ...<br />Setting up x11proto-dri2-dev (2.8-2) ...<br />Setting up x11proto-gl-dev (1.4.17-1) ...<br />Setting up x11proto-xext-dev (7.3.0-1) ...<br />Setting up libxext-dev:amd64 (2:1.3.3-1) ...<br />Setting up x11proto-xf86vidmode-dev (2.3.1-2) ...<br />Setting up libxxf86vm-dev:amd64 (1:1.1.4-1) ...<br />Setting up x11proto-fixes-dev (1:5.0-2ubuntu2) ...<br />Setting up libxfixes-dev:amd64 (1:5.0.1-2) ...<br />Setting up x11proto-damage-dev (1:1.2.1-2) ...<br />Setting up libxdamage-dev:amd64 (1:1.1.4-2) ...<br />Setting up libxcb-glx0-dev:amd64 (1.11.1-1ubuntu1) ...<br />Setting up libxcb-dri2-0-dev:amd64 (1.11.1-1ubuntu1) ...<br />Setting up libxcb-dri3-dev:amd64 (1.11.1-1ubuntu1) ...<br />Setting up libxcb-render0-dev:amd64 (1.11.1-1ubuntu1) ...<br />Setting up libxcb-randr0-dev:amd64 (1.11.1-1ubuntu1) ...<br />Setting up libxcb-shape0-dev:amd64 (1.11.1-1ubuntu1) ...<br />Setting up libxcb-xfixes0-dev:amd64 (1.11.1-1ubuntu1) ...<br />Setting up libxcb-sync-dev:amd64 (1.11.1-1ubuntu1) ...<br />Setting up libxcb-present-dev:amd64 (1.11.1-1ubuntu1) ...<br />Setting up libxshmfence-dev:amd64 (1.2-1) ...<br />Setting up libx11-xcb-dev:amd64 (2:1.6.3-1ubuntu2) ...<br />Setting up libwayland-bin (1.12.0-1~ubuntu16.04.3) ...<br />Setting up libwayland-dev:amd64 (1.12.0-1~ubuntu16.04.3) ...<br />Setting up libmircore-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...<br />Setting up libprotobuf9v5:amd64 (2.6.1-1.3) ...<br />Setting up libprotobuf-dev:amd64 (2.6.1-1.3) ...<br />Setting up libxkbcommon-dev (0.5.0-1ubuntu2) ...<br />Setting up libmircommon-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...<br />Setting up libmircookie2:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...<br />Setting up libmircookie-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...<br />Setting up libmirclient-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...<br />Setting up libegl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...<br />Setting up libgles2-mesa:amd64 (17.2.8-0ubuntu0~16.04.1) ...<br />Setting up libgles2-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...<br />Setting up mesa-common-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...<br />Setting up libgl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...<br />Setting up libglu1-mesa-dev:amd64 (9.0.0-2.1) ...<br />Setting up libqt5concurrent5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...<br />Setting up libqt5opengl5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...<br />Setting up libqt5printsupport5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...<br />Setting up libqt5sql5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...<br />Setting up libqt5test5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...<br />Setting up libqt5xml5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...<br />Setting up qt5-qmake:amd64 (5.5.1+dfsg-16ubuntu7.5) ...<br />Setting up qtbase5-dev-tools (5.5.1+dfsg-16ubuntu7.5) ...<br />Setting up qtbase5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...<br />Setting up libqt5opengl5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...<br />Setting up libqt5sql5-sqlite:amd64 (5.5.1+dfsg-16ubuntu7.5) ...<br />Setting up qttranslations5-l10n (5.5.1-2build1) ...<br />Processing triggers for libc-bin (2.23-0ubuntu10) ...<br />➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Bandage.git<br />Cloning into 'Bandage'...<br />remote: Counting objects: 7813, done.<br />remote: Total 7813 (delta 0), reused 0 (delta 0), pack-reused 7813<br />Receiving objects: 100% (7813/7813), 27.43 MiB | 16.33 MiB/s, done.<br />Resolving deltas: 100% (5973/5973), done.<br />Checking connectivity... done.<br />➜ Tools git:(master) ✗ cd Bandage&nbsp;<br />➜ Bandage git:(master) ls<br />Bandage.pro BandageTests.pro blast build_scripts command_line COPYING graph images ogdf program README.md tests ui<br />➜ Bandage git:(master) export QT_SELECT=5<br />➜ Bandage git:(master) qmake<br />➜ Bandage git:(master) ✗ make<br />/home/urbe/anaconda3/bin/uic ui/mainwindow.ui -o ui_mainwindow.h<br />/home/urbe/anaconda3/bin/uic ui/settingsdialog.ui -o ui_settingsdialog.h<br />/home/urbe/anaconda3/bin/uic ui/aboutdialog.ui -o ui_aboutdialog.h<br />/home/urbe/anaconda3/bin/uic ui/enteroneblastquerydialog.ui -o ui_enteroneblastquerydialog.h<br />/home/urbe/anaconda3/bin/uic ui/blastsearchdialog.ui -o ui_blastsearchdialog.h<br />/home/urbe/anaconda3/bin/uic ui/myprogressdialog.ui -o ui_myprogressdialog.h<br />/home/urbe/anaconda3/bin/uic ui/pathspecifydialog.ui -o ui_pathspecifydialog.h<br />/home/urbe/anaconda3/bin/uic ui/querypathsdialog.ui -o ui_querypathsdialog.h<br />/home/urbe/anaconda3/bin/uic ui/blasthitfiltersdialog.ui -o ui_blasthitfiltersdialog.h<br />/home/urbe/anaconda3/bin/uic ui/changenodenamedialog.ui -o ui_changenodenamedialog.h<br />/home/urbe/anaconda3/bin/uic ui/graphinfodialog.ui -o ui_graphinfodialog.h<br />/home/urbe/anaconda3/bin/uic ui/changenodedepthdialog.ui -o ui_changenodedepthdialog.h<br />g++ -c -pipe -O2 -std=gnu++0x -Wall -W -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -I. -Iui -I/usr/include -I../../anaconda3/include/qt -I../../anaconda3/include/qt/QtSvg -I../../anaconda3/include/qt/QtWidgets -I../../anaconda3/include/qt/QtGui -I../../anaconda3/include/qt/QtCore -I. -I. -I../../anaconda3/mkspecs/linux-g++ -o main.o program/main.cpp<br />g++ -c -pipe -O2 -std=gnu++0x -Wall -W -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -I. -Iui -I/usr/include -I../../anaconda3/include/qt -I../../anaconda3/include/qt/QtSvg -I../../anaconda3/include/qt/QtWidgets -I../../anaconda3/include/qt/QtGui -I../../anaconda3/include/qt/QtCore -I. -I. -I../../anaconda3/mkspecs/linux-g++ -o settings.o program/settings.cpp<br />....</p><p>...<br />g++ -Wl,-O1 -Wl,-rpath,/home/urbe/anaconda3/lib -o Bandage main.o settings.o globals.o graphlayoutworker.o debruijnnode.o debruijnedge.o graphicsitemnode.o graphicsitemedge.o mainwindow.o graphicsviewzoom.o settingsdialog.o mygraphicsview.o mygraphicsscene.o aboutdialog.o enteroneblastquerydialog.o blasthit.o blastqueries.o blastsearchdialog.o infotextwidget.o assemblygraph.o verticalscrollarea.o myprogressdialog.o nodewidthvisualaid.o verticallabel.o load.o image.o commoncommandlinefunctions.o mytablewidget.o buildblastdatabaseworker.o colourbutton.o blastquery.o runblastsearchworker.o blastsearch.o path.o pathspecifydialog.o graphlocation.o tablewidgetitemint.o tablewidgetitemdouble.o tablewidgetitemshown.o memory.o querypathspushbutton.o querypathsdialog.o blastquerypath.o blasthitfiltersdialog.o scinot.o changenodenamedialog.o querypathsequencecopybutton.o querypaths.o info.o reduce.o Graph.o GraphAttributes.o FMMMLayout.o geometry.o ClusterGraphAttributes.o FruchtermanReingold.o NMM.o GmlParser.o simple_graph_alg.o basic.o XmlParser.o String.o Hashing.o PoolMemoryAllocator.o GraphCopy.o CombinatorialEmbedding.o OgmlParser.o ClusterGraph.o Math.o EdgeAttributes.o NodeAttributes.o MAARPacking.o Multilevel.o numexcept.o Set.o Ogml.o DinoXmlParser.o DinoXmlScanner.o DinoTools.o DinoLineBuffer.o System.o QuadTreeNM.o QuadTreeNodeNM.o Constraint.o MultilevelGraph.o graphinfodialog.o tablewidgetitemname.o changenodedepthdialog.o qrc_images.o moc_graphlayoutworker.o moc_mainwindow.o moc_graphicsviewzoom.o moc_settingsdialog.o moc_mygraphicsview.o moc_mygraphicsscene.o moc_aboutdialog.o moc_enteroneblastquerydialog.o moc_blastquery.o moc_blastsearchdialog.o moc_infotextwidget.o moc_assemblygraph.o moc_verticalscrollarea.o moc_myprogressdialog.o moc_nodewidthvisualaid.o moc_verticallabel.o moc_mytablewidget.o moc_buildblastdatabaseworker.o moc_colourbutton.o moc_runblastsearchworker.o moc_pathspecifydialog.o moc_querypathspushbutton.o moc_querypathsdialog.o moc_blasthitfiltersdialog.o moc_changenodenamedialog.o moc_querypathsequencecopybutton.o moc_graphinfodialog.o moc_changenodedepthdialog.o -L/usr/lib -L/home/urbe/anaconda3/lib -lQt5Svg -lQt5Widgets -lQt5Gui -lQt5Core -lGL -lpthread&nbsp;<br />➜ Bandage git:(master) ✗ ls&nbsp;<br />aboutdialog.o DinoTools.o Makefile moc_infotextwidget.cpp moc_verticalscrollarea.o scinot.o<br />assemblygraph.o DinoXmlParser.o Math.o moc_infotextwidget.o MultilevelGraph.o Set.o<br />Bandage DinoXmlScanner.o memory.o moc_mainwindow.cpp Multilevel.o settingsdialog.o<br />Bandage.pro EdgeAttributes.o moc_aboutdialog.cpp moc_mainwindow.o mygraphicsscene.o settings.o<br />BandageTests.pro enteroneblastquerydialog.o moc_aboutdialog.o moc_mygraphicsscene.cpp mygraphicsview.o simple_graph_alg.o<br />basic.o FMMMLayout.o moc_assemblygraph.cpp moc_mygraphicsscene.o myprogressdialog.o String.o<br />blast FruchtermanReingold.o moc_assemblygraph.o moc_mygraphicsview.cpp mytablewidget.o System.o<br />blasthitfiltersdialog.o geometry.o moc_blasthitfiltersdialog.cpp moc_mygraphicsview.o NMM.o tablewidgetitemdouble.o<br />blasthit.o globals.o moc_blasthitfiltersdialog.o moc_myprogressdialog.cpp NodeAttributes.o tablewidgetitemint.o<br />blastqueries.o GmlParser.o moc_blastquery.cpp moc_myprogressdialog.o nodewidthvisualaid.o tablewidgetitemname.o<br />blastquery.o graph moc_blastquery.o moc_mytablewidget.cpp numexcept.o tablewidgetitemshown.o<br />blastquerypath.o GraphAttributes.o moc_blastsearchdialog.cpp moc_mytablewidget.o ogdf tests<br />blastsearchdialog.o GraphCopy.o moc_blastsearchdialog.o moc_nodewidthvisualaid.cpp Ogml.o ui<br />blastsearch.o graphicsitemedge.o moc_buildblastdatabaseworker.cpp moc_nodewidthvisualaid.o OgmlParser.o ui_aboutdialog.h<br />buildblastdatabaseworker.o graphicsitemnode.o moc_buildblastdatabaseworker.o moc_pathspecifydialog.cpp path.o ui_blasthitfiltersdialog.h<br />build_scripts graphicsviewzoom.o moc_changenodedepthdialog.cpp moc_pathspecifydialog.o pathspecifydialog.o ui_blastsearchdialog.h<br />changenodedepthdialog.o graphinfodialog.o moc_changenodedepthdialog.o moc_querypathsdialog.cpp PoolMemoryAllocator.o ui_changenodedepthdialog.h<br />changenodenamedialog.o graphlayoutworker.o moc_changenodenamedialog.cpp moc_querypathsdialog.o program ui_changenodenamedialog.h<br />ClusterGraphAttributes.o graphlocation.o moc_changenodenamedialog.o moc_querypathsequencecopybutton.cpp qrc_images.cpp ui_enteroneblastquerydialog.h<br />ClusterGraph.o Graph.o moc_colourbutton.cpp moc_querypathsequencecopybutton.o qrc_images.o ui_graphinfodialog.h<br />colourbutton.o Hashing.o moc_colourbutton.o moc_querypathspushbutton.cpp QuadTreeNM.o ui_mainwindow.h<br />CombinatorialEmbedding.o image.o moc_enteroneblastquerydialog.cpp moc_querypathspushbutton.o QuadTreeNodeNM.o ui_myprogressdialog.h<br />command_line images moc_enteroneblastquerydialog.o moc_runblastsearchworker.cpp querypathsdialog.o ui_pathspecifydialog.h<br />commoncommandlinefunctions.o info.o moc_graphicsviewzoom.cpp moc_runblastsearchworker.o querypathsequencecopybutton.o ui_querypathsdialog.h<br />Constraint.o infotextwidget.o moc_graphicsviewzoom.o moc_settingsdialog.cpp querypaths.o ui_settingsdialog.h<br />COPYING load.o moc_graphinfodialog.cpp moc_settingsdialog.o querypathspushbutton.o verticallabel.o<br />debruijnedge.o MAARPacking.o moc_graphinfodialog.o moc_verticallabel.cpp README.md verticalscrollarea.o<br />debruijnnode.o main.o moc_graphlayoutworker.cpp moc_verticallabel.o reduce.o XmlParser.o<br />DinoLineBuffer.o mainwindow.o moc_graphlayoutworker.o moc_verticalscrollarea.cpp runblastsearchworker.o<br />➜ Bandage git:(master) ✗ ./Bandage</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36880/jvarkit-java-utilities-for-bioinformatics</guid>
	<pubDate>Fri, 08 Jun 2018 09:31:55 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36880/jvarkit-java-utilities-for-bioinformatics</link>
	<title><![CDATA[Jvarkit : Java utilities for Bioinformatics]]></title>
	<description><![CDATA[Collection of Java tool kits for bioinformatics works:

Jvarkit : Java utilities for Bioinformatics<p>Address of the bookmark: <a href="http://lindenb.github.io/jvarkit/" rel="nofollow">http://lindenb.github.io/jvarkit/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/37905/phased-human-genome-assembly</guid>
	<pubDate>Mon, 08 Oct 2018 09:10:54 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/37905/phased-human-genome-assembly</link>
	<title><![CDATA[Phased Human Genome Assembly !]]></title>
	<description><![CDATA[<p>The new publicly available assembly (PacBio&nbsp;<a href="https://www.globenewswire.com/Tracker?data=IM2cKfZgtHafORdb9VSstujBjyW-aIzFILCtXNAkcY_yqVmxdjvG01R_FZQC7zLxs-alqquXwsW6MG98G9-g-ym8Nue2pmUZMtkIg3FIat2mYbJ-z2Ra367GlinbO13x" target="_blank" title=""><span style="text-decoration: underline;">HG00733</span></a>) has the fewest gaps of any human genome assembly, with more than half of the genome contained in gapless sequence at least 27 Mb long. The primary contig assembly is 2.89 Gb long and consists of 865 contigs that were assembled with PacBio data generated with the company&rsquo;s Sequel<span>&reg;</span>&nbsp;System. Using the&nbsp;<a href="https://www.globenewswire.com/Tracker?data=jOa6mE1Y5r8VbU1CaCgx1A0HsoVzJ7waxOiDKgvmKL6cwJq_eH4nWrGj2vLkNpxHl1-5CH4htDB4113PXT8WU60hvHQ-KKpvAwQwveEGvz3N4d0q7QHSa_X97LW8_9xEiYqfsc4d24ca-IpVYZsf7Ue-XL7fSIIZw_EHK-F96t1aaQNRcD-z1PP5qvlZbVwX" target="_blank" title=""><span style="text-decoration: underline;">FALCON-Unzip assembler</span></a>, maternal and paternal haplotypes were resolved over more than 80% of the genome. Maternal and paternal haplotype blocks were then further phased using Hi-C technology and the&nbsp;<a href="https://www.globenewswire.com/Tracker?data=jOa6mE1Y5r8VbU1CaCgx1IrQmRcKvNQm83FLTqQE6OGzutM-fEggnm4Z-nsniK0D_YmDKS_UKWE0NHtHbgvbL973Y2-9NhrWhYKizXQ4lpiTvlqPf1UZdjqVs7BDjISgDnovv8foYw8es8jQzAg5Xfq1CH36NOnWQgA_X04XSvyEEEj0q801Im6cV5M5K4eL15vb_ZgUayccOvDY_fc6lxxPAAAyA4h16-zUN44Y81KdujciCrJrv5xynMIXEjRsaIKCf6eCX_Q1j_uZlN5TD0MVr6HulTYG8lGgyL0x-eQ=" target="_blank" title=""><span style="text-decoration: underline;">FALCON-Phase method</span></a>developed in collaboration with Phase Genomics. The genome was then&nbsp;<em>de novo</em>&nbsp;scaffolded using Phase Genomics&rsquo;&nbsp;<a href="https://www.globenewswire.com/Tracker?data=4wcqEWHJpCHRJARQkC0oVkYT9htT14iVebujxcW1nMpAjmigHGQ46ObCGetRfyaZm1ADIHaV1-30B9izTAhjJ-efhFlxorUxs08kdV-9AAzQyuHJ9S7wxnRRnyegsTZd" target="_blank" title=""><span style="text-decoration: underline;">Proximo Hi-C platform</span></a>, resulting in the first chromosome-scale diploid assembly of a single individual accomplished with only two technologies. More specific details about the assembly are included on the PacBio blog.</p><p>The data are available using NCBI accession IDs: BioProject: (<a href="https://www.globenewswire.com/Tracker?data=YZtCuhY2wu5H0yIso9jtUufPXbwyHh1QOZ1jBggGpK5NtXaU_JGC9X39F3uHZ96uVmu6hW5OB2Qq805hUEW2OhSNCm630yFiEF6_nsAwYB0=" target="_blank" title=""><span style="text-decoration: underline;">PRJNA483067</span></a>), assembly: [<a href="https://www.globenewswire.com/Tracker?data=CEXZ7E56JOsRgfH4Wq3r5LVbv4QH_UIekV9idYBys9l8K7pFft824jmYWNzJqK7lQ9fMbaAtbURpm8gM7zqUbpPUrydFwrkJGGtG-NBHctjyjddiFY-p06xZPm2mHXE2" target="_blank" title=""><span style="text-decoration: underline;">RBJD00000000</span></a>] and sequence data (<a href="https://www.globenewswire.com/Tracker?data=pELP2RpqTqTRaPF9yN1N7GZYlQmTxpY0aW-B8xaNw6iyD-Lylw7X3UzMDK3YS4AIYgLtD13em2XsbzOwKhXuNbI4Ks6-LSyXl1_yVdFoB0U=" target="_blank" title=""><span style="text-decoration: underline;">SRP155659</span></a>).</p><p><span>Additional Resources</span></p><ul>
<li><a href="http://globenewswire.com/Tracker?data=zXpdadphSgIAIEWeq46yRPm5-TU0H7wTkL48ue4I9GsaHd5mJyMb9PgXgAsElREkLOCOdWdJ8uW9DHB-LyQ7xhzbd97Qis6CuAlqD0ubGgY%3D" target="_blank" title=""><span style="text-decoration: underline;">Interactive map</span></a>&nbsp;showcasing global initiatives underway to generate reference-quality human genome assemblies for diverse populations</li>
<li><a href="http://globenewswire.com/Tracker?data=EQ8NIaaa8k1Nw1MPRJYIHYrqgsDy92kU8W0siJdGQhq5IJ0dcb890PFFm-C1SrAlFf0xkxUVRxZefFK5ebhoIzmS-6OjR1G9sTxOkCOwRHCAZWmHL-e7uGSuZYcw1VsDp8AeDWO0RwcepMMB6hAoR6BBCJDiJVVZtdFlWBn2uxs%3D" target="_blank" title=""><span style="text-decoration: underline;">BioReport Podcast</span></a>&nbsp;on the value of ethnic-specific reference genomes</li>
<li><em>Nature Reviews Genetics</em>&nbsp;paper from NHGRI:&nbsp;<a href="http://globenewswire.com/Tracker?data=dffu-wPD_JX1_KVeCA6VFy-kP1tlAUbn7d85saXD59dnnJfT2BE3N_Rbm6kT4BvifA_XEs49ioa75cy4HyFi90RA_LRa2QFF6Y4mr-dcoMucljZw0K4JNDZuwWkWPE51cVC2Lqq3E3C1aZ8un6Bq3i-OO_NiVH0hh23hUw4wC84%3D" target="_blank" title=""><span style="text-decoration: underline;">Prioritizing&nbsp;diversity&nbsp;in human genomics research</span></a></li>
<li>Article in&nbsp;<em>The Journal of Precision Medicine</em>: &ldquo;<a href="http://globenewswire.com/Tracker?data=yokLqO2TCBLCdj6uZl-GYbqcGMWBerBYjSPrLMumNrWF2p5XlXq9yl5p-1b5xx3Ckfn5ZjQWkdhxLttbiNae5gccUCP-9RWPUqvTu9MuU9zgJ1c8e14lAladCuEOiVZ2oVRiqssPtLu9hgQWw4ad5EUxZemevsHE4BHC6IiFmMZ6DS6ApwZu-IonFgCFBIcjWOpitQthDASosfaqkMi9LsKgLU9F0WGVJDDOzHXpddhjfCUdEEJ7xC1p8uh9TSiCZgZV6XPlUJSe8n0C_9TtOw%3D%3D" target="_blank" title=""><span style="text-decoration: underline;">Minority Report &ndash; Ethnic Diversity and the Real Promise for Precision Medicine</span></a>&rdquo;</li>
<li>Article&nbsp;in&nbsp;<em>Bio-IT World</em>: &ldquo;<a href="http://globenewswire.com/Tracker?data=rLp1pKetctTPitNEnRjOVDZ3Cvw3FUdL6_ybXncvhjR4ksOrX3y6HUK8WtLlKHT7XZzq_woUjZ-uw20YNvsP0GZAmy5lVqETt27oBLi02wFtTH_6ubELIHtBu8vfVyKnqKp-YhosFG5K7y0RUtzmNjOAlCYPAeVXabn2a2AiSePxUXA_tSy_g79hjYm63x9dPN9oFQGYedOsyHD_ls8DKw%3D%3D" target="_blank" title=""><span style="text-decoration: underline;">Genomic Data Standards Are a Necessity</span></a>&rdquo;</li>
<li>NHGRI Project Award:&nbsp;<a href="http://globenewswire.com/Tracker?data=FbqTEeRffJ88lFryYX6MiOefXvIXFdZDAyW4nrFoYNHaJyMEYIcb7I4BIcEQmxzsKOjrlf9F8irfRJeJLOqG8KFsl-kvkhakUkg3BfYdKGnpLzKYyWbUFR0aKMeEXirHBi7oDLEUSDO45qxANwxyee-pqZXfzAIwF1Wcuaf7EIzNqRqmBUJ3TyNyI05lwAo9gDKmApMnJo5VxPj5P_6rY8lisuv1PNSAh_kJPOuhVBk%3D" target="_blank" title=""><span style="text-decoration: underline;">High Quality Human and Non-Human Primate Genome Assemblies</span></a></li>
</ul><p>More details are available on the PacBio website:</p><ul>
<li>Blog post:&nbsp;<a href="http://globenewswire.com/Tracker?data=ycj-ujgsKzVyljNa11buVmIS5tk9B733VsFZEw77nBXo-IkBvcoG16dN9vuTiY3nm2G5dJZS5Iva3w_znrEtJVDuU8cVlFpozY2ibinKwrMGxkXZVSqW8_uD8fbySRjM5Q_cjuPU22ARFSSLCc9vHJx9WHnb9Rza-qPbuWgewa0rWWStq2fQY5mLpeaQf5fcDJnyQkvDAMI3fauXdzyThg%3D%3D" target="_blank" title=""><span style="text-decoration: underline;">Data Release: Highest-Quality, Most Contiguous Individual Human Genome Assembly to Date</span></a></li>
<li>Blog post:&nbsp;<a href="http://globenewswire.com/Tracker?data=GlZZ9nyp5mDSjJPPfhVD1-dZ_W2l8s0eAUox3TQs949zyGjzO7dx9xodyvyqerdqPC-G3ZhdPEs9xNhJwflrwgHPYQL3kTofprKHBBq3O4gn9E75YUBweJw9b6tTE89sMLUQzF-vRNNDjero3mibm_uG-fSHoYBTm2ZlyEmwzZ5E9tXVd5_RjG0Xnej2E0scA0SncEItAF6Q7vdOydTV_Yr9yYT2TmKY5jtyAt6ZrNGn3McqfV9mMRkR-8dYJLqrQln9JiEkWTwUae6Blj56HyjyXKl6Dfa_CyNuy4r-EWU%3D" target="_blank" title=""><span style="text-decoration: underline;">For Reference-Grade Human Genome Assemblies, SMRT Sequencing Yields Optimal Results</span></a></li>
<li>Webinar: &nbsp;<a href="http://globenewswire.com/Tracker?data=xlnfDwMNLGZZvtexJYsUgMe-DV8HNrYx2QqjwIjfj40dToVtqrBi-gvhknHZmIe8GV_3WU3_9LIlP6GzG3ZoajnDIpwECzdMV5Vyy8Ast4Y2AiHJckf7rBhZVEU4_mV4JB0k3I9XjN2jHK8Cp5uBxyIWWqPdI6qBBdCYYhYLXUTkKpaZEV98oCfC5ET2Q7OSwUM7NieKa75yzMHwaPEYwg%3D%3D" target="_blank" title=""><span style="text-decoration: underline;">Assembling High-Quality Human Reference Genomes for Global Populations</span></a></li>
<li>FALCON-Phase&nbsp;<a href="http://globenewswire.com/Tracker?data=4Z9LDdRq3w2zYFQXEFGmz6u-Vrbfh96syfzrQMKhegLRo2PUvk7s3Xz_y1o--NuTLoCQMrHsqOEBUHIL1IPeOmhyf6Eqwdp8dv8xYo9gSVI%3D" target="_blank" title=""><span style="text-decoration: underline;">press release</span></a>&nbsp;and article&nbsp;<a href="http://globenewswire.com/Tracker?data=4Z9LDdRq3w2zYFQXEFGmz9Ts_IJqHWWrKd33x_ldJEU9mSKXpcVTTi9ioY0kVqrbrXHeCKDf4TdPnAoPJaGBK3YeZtYp-nXZacgyPESZ1XboSUZEJ9rIhDyW7bTLL5HN" target="_blank" title=""><span style="text-decoration: underline;">preprint</span></a></li>
<li>PacBio research focus webpage about&nbsp;<a href="http://globenewswire.com/Tracker?data=E-zzUkw4N01KR4muPun47qg4HX8ToDvLS4sX953hLM2wRyQZ2upkLR4WidyXTFDRLWQORpqxnkbD-CNzsOJyIfH8mJPbrLwRf04J4yjuNdem-Fulc8QIT3OCi4wx5LpqgC2ymLE0rYX5UOpbFPBgvA%3D%3D" target="_blank" title=""><span style="text-decoration: underline;">Human Population Genetics</span></a></li>
</ul><p>&nbsp;Ref:&nbsp;https://stockguru.com/2018/10/08/pacific-biosciences-releases-highest-quality-most-contiguous-individual-human-genome-assembly-to-date/</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38063/referee-genome-assembly-quality-scores</guid>
	<pubDate>Sun, 04 Nov 2018 16:44:30 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38063/referee-genome-assembly-quality-scores</link>
	<title><![CDATA[Referee: Genome assembly quality scores]]></title>
	<description><![CDATA[<p>Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site in an assembled genome to calculate a quality score for each position in the genome assembly.</p>
<p>We accomplish this by first calculating genotype likelihoods for every site. For a given site in a diploid genome, there are 10 possible genotypes (AA, AC, AG, AT, CC, CG, CT, GG, GT, TT). Referee takes as input the genotype likelihoods calculated for all 10 genotypes given the called reference base at each position.</p>
<h3>Referee is a program to calculate a quality score for every position in a genome assembly. This allows for easy filtering of low quality sites for any downstream analysis.</h3>
<p>https://github.com/gwct/referee</p><p>Address of the bookmark: <a href="https://gwct.github.io/referee/#" rel="nofollow">https://gwct.github.io/referee/#</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38441/genome-sequence-based-sub-species-delineation</guid>
	<pubDate>Wed, 12 Dec 2018 08:31:14 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38441/genome-sequence-based-sub-species-delineation</link>
	<title><![CDATA[Genome sequence-based (sub-)species delineation.]]></title>
	<description><![CDATA[<p>The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also calculates differences in genomic G+C content.</p>
<p>http://ggdc.dsmz.de/ggdc_background.php#</p>
<p><small>Genome-to-Genome Distance Calculator 2.1</small></p>
<p>http://ggdc.dsmz.de/ggdc.php</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="http://ggdc.dsmz.de/" rel="nofollow">http://ggdc.dsmz.de/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>

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