Address of the bookmark: https://github.com/combogenomics/medusa

1. Ensure the package lists are up-to-date: sudo apt-get update
2. Install prerequisite packages: sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev
3. Download the Bandage code from GitHub: git clone https://github.com/rrwick/Bandage.git
4. Open a terminal in the Bandage directory.
5. Set the environment variable to specify that you will be using Qt 5, not Qt 4: export QT_SELECT=5
6. Run qmake to generate a Makefile: qmake
7. Build the program: make
8. Bandage should now be an executable file.
9. Optionally, copy the program into /usr/local/bin: sudo make install. The Bandage build directory can then be deleted.

➜ Tools git:(master) ✗ sudo apt-get update
[sudo] password for urbe: 
Hit:1 http://ppa.launchpad.net/webupd8team/atom/ubuntu xenial InRelease
Get:2 http://security.ubuntu.com/ubuntu xenial-security InRelease [107 kB] 
Hit:3 http://ppa.launchpad.net/webupd8team/java/ubuntu xenial InRelease 
Hit:4 http://be.archive.ubuntu.com/ubuntu xenial InRelease 
Get:5 http://be.archive.ubuntu.com/ubuntu xenial-updates InRelease [109 kB]
Get:6 http://be.archive.ubuntu.com/ubuntu xenial-backports InRelease [107 kB] 
Get:7 https://cran.rstudio.com/bin/linux/ubuntu xenial/ InRelease [3.590 B] 
Hit:8 https://download.docker.com/linux/ubuntu xenial InRelease 
Ign:9 http://download.opensuse.org/repositories/home:/sionescu/Debian ./ InRelease 
Hit:10 http://download.opensuse.org/repositories/home:/sionescu/Debian ./ Release 
Get:11 http://packages.cloud.google.com/apt cloud-sdk-xenial InRelease [6.372 B]
Get:12 http://security.ubuntu.com/ubuntu xenial-security/main amd64 Packages [484 kB]
Get:13 http://security.ubuntu.com/ubuntu xenial-security/main i386 Packages [433 kB]
Get:14 http://security.ubuntu.com/ubuntu xenial-security/main Translation-en [209 kB]
Get:15 http://security.ubuntu.com/ubuntu xenial-security/main amd64 DEP-11 Metadata [67,5 kB]
Get:16 http://security.ubuntu.com/ubuntu xenial-security/main DEP-11 64x64 Icons [68,0 kB] 
Get:17 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 DEP-11 Metadata [107 kB]
Get:18 http://security.ubuntu.com/ubuntu xenial-security/universe DEP-11 64x64 Icons [147 kB]
Get:19 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages [769 kB] 
Get:20 http://be.archive.ubuntu.com/ubuntu xenial-updates/main i386 Packages [710 kB] 
Get:21 http://be.archive.ubuntu.com/ubuntu xenial-updates/main Translation-en [319 kB]
Get:22 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 DEP-11 Metadata [319 kB]
Get:24 http://be.archive.ubuntu.com/ubuntu xenial-updates/main DEP-11 64x64 Icons [228 kB] 
Get:25 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 DEP-11 Metadata [246 kB]
Err:11 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
Get:26 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe DEP-11 64x64 Icons [331 kB]
Get:27 http://be.archive.ubuntu.com/ubuntu xenial-updates/multiverse amd64 DEP-11 Metadata [5.964 B]
Get:28 http://be.archive.ubuntu.com/ubuntu xenial-backports/main amd64 DEP-11 Metadata [3.328 B]
Get:29 http://be.archive.ubuntu.com/ubuntu xenial-backports/universe amd64 DEP-11 Metadata [5.088 B]
Fetched 4.779 kB in 2s (1.606 kB/s) 
Reading package lists... Done
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
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
W: Some index files failed to download. They have been ignored, or old ones used instead.
➜ Tools git:(master) ✗ sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev
Reading package lists... Done
Building dependency tree 
Reading state information... Done
build-essential is already the newest version (12.1ubuntu2).
git is already the newest version (1:2.7.4-0ubuntu1.3).
The following packages were automatically installed and are no longer required:
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
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
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
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
libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5printsupport5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5test5 libqt5widgets5 libqt5xml5 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 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 qt5-qmake
qtbase5-dev-tools qttranslations5-l10n x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-xext-dev x11proto-xf86vidmode-dev
Suggested packages:
libqt5libqgtk2 qt5-image-formats-plugins qtwayland5 libxext-doc libmysqlclient-dev libpq-dev libsqlite3-dev unixodbc-dev
The following NEW packages will be installed:
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
libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5printsupport5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5svg5-dev libqt5test5 libqt5widgets5 libqt5xml5
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
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
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
0 upgraded, 64 newly installed, 0 to remove and 11 not upgraded.
Need to get 15,2 MB of archives.
After this operation, 78,5 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5core5a amd64 5.5.1+dfsg-16ubuntu7.5 [1.817 kB]
Get:2 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5dbus5 amd64 5.5.1+dfsg-16ubuntu7.5 [175 kB]
Get:3 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5network5 amd64 5.5.1+dfsg-16ubuntu7.5 [540 kB]
Get:4 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-icccm4 amd64 0.4.1-1ubuntu1 [10,4 kB]
Get:5 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-image0 amd64 0.4.0-1build1 [12,3 kB]
Get:6 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-keysyms1 amd64 0.4.0-1 [8.406 B]
Get:7 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-randr0 amd64 1.11.1-1ubuntu1 [14,4 kB]
Get:8 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-render-util0 amd64 0.3.9-1 [9.638 B]
Get:9 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-xkb1 amd64 1.11.1-1ubuntu1 [29,2 kB]
Get:10 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxkbcommon-x11-0 amd64 0.5.0-1ubuntu2 [13,5 kB]
Get:11 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5gui5 amd64 5.5.1+dfsg-16ubuntu7.5 [2.290 kB]
Get:12 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5widgets5 amd64 5.5.1+dfsg-16ubuntu7.5 [2.252 kB]
Get:13 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libqt5svg5 amd64 5.5.1-2build1 [128 kB]
Get:14 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libqt5svg5-dev amd64 5.5.1-2build1 [9.724 B]
Get:15 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libdrm-dev amd64 2.4.83-1~16.04.1 [229 kB]
Get:16 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-dri2-dev all 2.8-2 [12,6 kB]
Get:17 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-gl-dev all 1.4.17-1 [17,9 kB]
Get:18 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-xext-dev all 7.3.0-1 [212 kB]
Get:19 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxext-dev amd64 2:1.3.3-1 [82,1 kB]
Get:20 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-xf86vidmode-dev all 2.3.1-2 [6.116 B]
Get:21 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxxf86vm-dev amd64 1:1.1.4-1 [13,3 kB]
Get:22 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-fixes-dev all 1:5.0-2ubuntu2 [14,2 kB]
Get:23 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxfixes-dev amd64 1:5.0.1-2 [10,9 kB]
Get:24 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 x11proto-damage-dev all 1:1.2.1-2 [8.286 B]
Get:25 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxdamage-dev amd64 1:1.1.4-2 [5.028 B]
Get:26 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-glx0-dev amd64 1.11.1-1ubuntu1 [26,9 kB]
Get:27 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-dri2-0-dev amd64 1.11.1-1ubuntu1 [8.384 B]
Get:28 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-dri3-dev amd64 1.11.1-1ubuntu1 [5.752 B]
Get:29 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-render0-dev amd64 1.11.1-1ubuntu1 [15,3 kB]
Get:30 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-randr0-dev amd64 1.11.1-1ubuntu1 [18,2 kB]
Get:31 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-shape0-dev amd64 1.11.1-1ubuntu1 [6.900 B]
Get:32 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-xfixes0-dev amd64 1.11.1-1ubuntu1 [11,2 kB]
Get:33 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-sync-dev amd64 1.11.1-1ubuntu1 [10,1 kB]
Get:34 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxcb-present-dev amd64 1.11.1-1ubuntu1 [6.618 B]
Get:35 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxshmfence-dev amd64 1.2-1 [3.676 B]
Get:36 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libx11-xcb-dev amd64 2:1.6.3-1ubuntu2 [9.730 B]
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]
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]
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]
Get:40 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libprotobuf9v5 amd64 2.6.1-1.3 [326 kB]
Get:41 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libprotobuf-dev amd64 2.6.1-1.3 [473 kB]
Get:42 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxkbcommon-dev amd64 0.5.0-1ubuntu2 [231 kB]
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]
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]
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]
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]
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]
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]
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]
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]
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]
Get:52 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libglu1-mesa-dev amd64 9.0.0-2.1 [202 kB]
Get:53 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5concurrent5 amd64 5.5.1+dfsg-16ubuntu7.5 [24,3 kB]
Get:54 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5opengl5 amd64 5.5.1+dfsg-16ubuntu7.5 [128 kB]
Get:55 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5printsupport5 amd64 5.5.1+dfsg-16ubuntu7.5 [174 kB]
Get:56 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5sql5 amd64 5.5.1+dfsg-16ubuntu7.5 [104 kB]
Get:57 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5test5 amd64 5.5.1+dfsg-16ubuntu7.5 [84,5 kB]
Get:58 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5xml5 amd64 5.5.1+dfsg-16ubuntu7.5 [91,8 kB]
Get:59 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qt5-qmake amd64 5.5.1+dfsg-16ubuntu7.5 [1.192 kB]
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]
Get:61 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qtbase5-dev amd64 5.5.1+dfsg-16ubuntu7.5 [931 kB]
Get:62 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5opengl5-dev amd64 5.5.1+dfsg-16ubuntu7.5 [31,5 kB]
Get:63 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5sql5-sqlite amd64 5.5.1+dfsg-16ubuntu7.5 [33,0 kB]
Get:64 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 qttranslations5-l10n all 5.5.1-2build1 [1.210 kB]
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➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Bandage.git
Cloning into 'Bandage'...
remote: Counting objects: 7813, done.
remote: Total 7813 (delta 0), reused 0 (delta 0), pack-reused 7813
Receiving objects: 100% (7813/7813), 27.43 MiB | 16.33 MiB/s, done.
Resolving deltas: 100% (5973/5973), done.
Checking connectivity... done.
➜ Tools git:(master) ✗ cd Bandage 
➜ Bandage git:(master) ls
Bandage.pro BandageTests.pro blast build_scripts command_line COPYING graph images ogdf program README.md tests ui
➜ Bandage git:(master) export QT_SELECT=5
➜ Bandage git:(master) qmake
➜ Bandage git:(master) ✗ make
/home/urbe/anaconda3/bin/uic ui/mainwindow.ui -o ui_mainwindow.h
/home/urbe/anaconda3/bin/uic ui/settingsdialog.ui -o ui_settingsdialog.h
/home/urbe/anaconda3/bin/uic ui/aboutdialog.ui -o ui_aboutdialog.h
/home/urbe/anaconda3/bin/uic ui/enteroneblastquerydialog.ui -o ui_enteroneblastquerydialog.h
/home/urbe/anaconda3/bin/uic ui/blastsearchdialog.ui -o ui_blastsearchdialog.h
/home/urbe/anaconda3/bin/uic ui/myprogressdialog.ui -o ui_myprogressdialog.h
/home/urbe/anaconda3/bin/uic ui/pathspecifydialog.ui -o ui_pathspecifydialog.h
/home/urbe/anaconda3/bin/uic ui/querypathsdialog.ui -o ui_querypathsdialog.h
/home/urbe/anaconda3/bin/uic ui/blasthitfiltersdialog.ui -o ui_blasthitfiltersdialog.h
/home/urbe/anaconda3/bin/uic ui/changenodenamedialog.ui -o ui_changenodenamedialog.h
/home/urbe/anaconda3/bin/uic ui/graphinfodialog.ui -o ui_graphinfodialog.h
/home/urbe/anaconda3/bin/uic ui/changenodedepthdialog.ui -o ui_changenodedepthdialog.h
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
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
....

...
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 
➜ Bandage git:(master) ✗ ls 
aboutdialog.o DinoTools.o Makefile moc_infotextwidget.cpp moc_verticalscrollarea.o scinot.o
assemblygraph.o DinoXmlParser.o Math.o moc_infotextwidget.o MultilevelGraph.o Set.o
Bandage DinoXmlScanner.o memory.o moc_mainwindow.cpp Multilevel.o settingsdialog.o
Bandage.pro EdgeAttributes.o moc_aboutdialog.cpp moc_mainwindow.o mygraphicsscene.o settings.o
BandageTests.pro enteroneblastquerydialog.o moc_aboutdialog.o moc_mygraphicsscene.cpp mygraphicsview.o simple_graph_alg.o
basic.o FMMMLayout.o moc_assemblygraph.cpp moc_mygraphicsscene.o myprogressdialog.o String.o
blast FruchtermanReingold.o moc_assemblygraph.o moc_mygraphicsview.cpp mytablewidget.o System.o
blasthitfiltersdialog.o geometry.o moc_blasthitfiltersdialog.cpp moc_mygraphicsview.o NMM.o tablewidgetitemdouble.o
blasthit.o globals.o moc_blasthitfiltersdialog.o moc_myprogressdialog.cpp NodeAttributes.o tablewidgetitemint.o
blastqueries.o GmlParser.o moc_blastquery.cpp moc_myprogressdialog.o nodewidthvisualaid.o tablewidgetitemname.o
blastquery.o graph moc_blastquery.o moc_mytablewidget.cpp numexcept.o tablewidgetitemshown.o
blastquerypath.o GraphAttributes.o moc_blastsearchdialog.cpp moc_mytablewidget.o ogdf tests
blastsearchdialog.o GraphCopy.o moc_blastsearchdialog.o moc_nodewidthvisualaid.cpp Ogml.o ui
blastsearch.o graphicsitemedge.o moc_buildblastdatabaseworker.cpp moc_nodewidthvisualaid.o OgmlParser.o ui_aboutdialog.h
buildblastdatabaseworker.o graphicsitemnode.o moc_buildblastdatabaseworker.o moc_pathspecifydialog.cpp path.o ui_blasthitfiltersdialog.h
build_scripts graphicsviewzoom.o moc_changenodedepthdialog.cpp moc_pathspecifydialog.o pathspecifydialog.o ui_blastsearchdialog.h
changenodedepthdialog.o graphinfodialog.o moc_changenodedepthdialog.o moc_querypathsdialog.cpp PoolMemoryAllocator.o ui_changenodedepthdialog.h
changenodenamedialog.o graphlayoutworker.o moc_changenodenamedialog.cpp moc_querypathsdialog.o program ui_changenodenamedialog.h
ClusterGraphAttributes.o graphlocation.o moc_changenodenamedialog.o moc_querypathsequencecopybutton.cpp qrc_images.cpp ui_enteroneblastquerydialog.h
ClusterGraph.o Graph.o moc_colourbutton.cpp moc_querypathsequencecopybutton.o qrc_images.o ui_graphinfodialog.h
colourbutton.o Hashing.o moc_colourbutton.o moc_querypathspushbutton.cpp QuadTreeNM.o ui_mainwindow.h
CombinatorialEmbedding.o image.o moc_enteroneblastquerydialog.cpp moc_querypathspushbutton.o QuadTreeNodeNM.o ui_myprogressdialog.h
command_line images moc_enteroneblastquerydialog.o moc_runblastsearchworker.cpp querypathsdialog.o ui_pathspecifydialog.h
commoncommandlinefunctions.o info.o moc_graphicsviewzoom.cpp moc_runblastsearchworker.o querypathsequencecopybutton.o ui_querypathsdialog.h
Constraint.o infotextwidget.o moc_graphicsviewzoom.o moc_settingsdialog.cpp querypaths.o ui_settingsdialog.h
COPYING load.o moc_graphinfodialog.cpp moc_settingsdialog.o querypathspushbutton.o verticallabel.o
debruijnedge.o MAARPacking.o moc_graphinfodialog.o moc_verticallabel.cpp README.md verticalscrollarea.o
debruijnnode.o main.o moc_graphlayoutworker.cpp moc_verticallabel.o reduce.o XmlParser.o
DinoLineBuffer.o mainwindow.o moc_graphlayoutworker.o moc_verticalscrollarea.cpp runblastsearchworker.o
➜ Bandage git:(master) ✗ ./Bandage

The data are available using NCBI accession IDs: BioProject: (PRJNA483067), assembly: [RBJD00000000] and sequence data (SRP155659).

Additional Resources

• Interactive map showcasing global initiatives underway to generate reference-quality human genome assemblies for diverse populations
• BioReport Podcast on the value of ethnic-specific reference genomes
• Nature Reviews Genetics paper from NHGRI: Prioritizing diversity in human genomics research
• Article in The Journal of Precision Medicine: “Minority Report – Ethnic Diversity and the Real Promise for Precision Medicine”
• Article in Bio-IT World: “Genomic Data Standards Are a Necessity”
• NHGRI Project Award: High Quality Human and Non-Human Primate Genome Assemblies

More details are available on the PacBio website:

• Blog post: Data Release: Highest-Quality, Most Contiguous Individual Human Genome Assembly to Date
• Blog post: For Reference-Grade Human Genome Assemblies, SMRT Sequencing Yields Optimal Results
• Webinar:  Assembling High-Quality Human Reference Genomes for Global Populations
• FALCON-Phase press release and article preprint
• PacBio research focus webpage about Human Population Genetics

 Ref: https://stockguru.com/2018/10/08/pacific-biosciences-releases-highest-quality-most-contiguous-individual-human-genome-assembly-to-date/

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

1. Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
2. Intact ordering and orienting of contigs.
3. Chimeric contig correction
4. GFF lift-over
5. Structural variant calling with and integrated version of Assemblytics
6. Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

MitoFinder is also designed to find and annotate mitochondrial sequences in existing genomic assemblies (generated from Hifi/PacBio/Nanopore/Illumina sequencing data...)

MitoFinder is distributed under the license.

Address of the bookmark: https://github.com/RemiAllio/MitoFinder

Address of the bookmark: https://github.com/cschin/Peregrine

Again, running spades.py will show you the options:

spades.py

This produces:

SPAdes genome assembler v3.10.1

Usage: /usr/local/SPAdes-3.10.1-Linux/bin/spades.py [options] -o <output_dir>

Basic options:
-o      <output_dir>    directory to store all the resulting files (required)
--sc                    this flag is required for MDA (single-cell) data
--meta                  this flag is required for metagenomic sample data
--rna                   this flag is required for RNA-Seq data
--plasmid               runs plasmidSPAdes pipeline for plasmid detection
--iontorrent            this flag is required for IonTorrent data
--test                  runs SPAdes on toy dataset
-h/--help               prints this usage message
-v/--version            prints version

Input data:
--12    <filename>      file with interlaced forward and reverse paired-end reads
-1      <filename>      file with forward paired-end reads
-2      <filename>      file with reverse paired-end reads
-s      <filename>      file with unpaired reads
--pe<#>-12      <filename>      file with interlaced reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-1       <filename>      file with forward reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-2       <filename>      file with reverse reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-s       <filename>      file with unpaired reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-<or>    orientation of reads for paired-end library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--s<#>          <filename>      file with unpaired reads for single reads library number <#> (<#> = 1,2,..,9)
--mp<#>-12      <filename>      file with interlaced reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-1       <filename>      file with forward reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-2       <filename>      file with reverse reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-s       <filename>      file with unpaired reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-<or>    orientation of reads for mate-pair library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--hqmp<#>-12    <filename>      file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-1     <filename>      file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-2     <filename>      file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-s     <filename>      file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-<or>  orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--nxmate<#>-1   <filename>      file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)
--nxmate<#>-2   <filename>      file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)
--sanger        <filename>      file with Sanger reads
--pacbio        <filename>      file with PacBio reads
--nanopore      <filename>      file with Nanopore reads
--tslr  <filename>      file with TSLR-contigs
--trusted-contigs       <filename>      file with trusted contigs
--untrusted-contigs     <filename>      file with untrusted contigs

Pipeline options:
--only-error-correction runs only read error correction (without assembling)
--only-assembler        runs only assembling (without read error correction)
--careful               tries to reduce number of mismatches and short indels
--continue              continue run from the last available check-point
--restart-from  <cp>    restart run with updated options and from the specified check-point ('ec', 'as', 'k<int>', 'mc')
--disable-gzip-output   forces error correction not to compress the corrected reads
--disable-rr            disables repeat resolution stage of assembling

Advanced options:
--dataset       <filename>      file with dataset description in YAML format
-t/--threads    <int>           number of threads
                                [default: 16]
-m/--memory     <int>           RAM limit for SPAdes in Gb (terminates if exceeded)
                                [default: 250]
--tmp-dir       <dirname>       directory for temporary files
                                [default: <output_dir>/tmp]
-k              <int,int,...>   comma-separated list of k-mer sizes (must be odd and
                                less than 128) [default: 'auto']
--cov-cutoff    <float>         coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']
--phred-offset  <33 or 64>      PHRED quality offset in the input reads (33 or 64)
                                [default: auto-detect]

As you can see this is also a “pipeline” of tools that can be switched on or off. SPAdes takes quite a long time, so for the purposes of this practical, something like this may suffice:

spades.py -t 4 \
          -m 32 \
          -k 31,51,71 \
          --only-assembler \
          -1 miseq.1.fastq -2 miseq.2.fastq \
          --nanopore minion.fastq \
          -o hybrid_assembly

In turn, these parameters mean

• use 4 threads
• max memory is 32Gb
• use 3 kmer values to build the de bruijn graph(s) - 31, 51 and 71
• only run the assembler, not the correction algorithm (for speed)
• read 1 and read 2 of the MiSeq data
• the nanopore data
• put the output in folder “hybrid_assembly”

Following are the genome assembly tools based on string graph:

1.SGA (String Graph Assembler) https://github.com/jts/sga

Assembles large genomes from high coverage short read data. SGA is designed as a modular set of programs, which are used to form an assembly pipeline. SGA implements a set of assembly algorithms based on the FM-index. As the FM-index is a compressed data structure, the algorithms are very memory efficient. The SGA assembly has three distinct phases. The first phase corrects base calling errors in the reads. The second phase assembles contigs from the corrected reads. The third phase uses paired end and/or mate pair data to build scaffolds from the contigs. The output of this software is a PDF report that allows the properties of the genome and data quality to be visually explored. By providing more information to the user at the start of an assembly project, this software will help increase awareness of the factors that make a given assembly easy or difficult, assist in the selection of software and parameters and help to troubleshoot an assembly if it runs into problems.

2. SAGE: String-overlap Assembly of GEnomes https://github.com/lucian-ilie/SAGE2

SAGE, for de novo genome assembly. As opposed to most assemblers, which are de Bruijn graph based, SAGE uses the string-overlap graph. SAGE builds upon great existing work on string-overlap graph and maximum likelihood assembly, bringing an important number of new ideas, such as the efficient computation of the transitive reduction of the string overlap graph, the use of (generalized) edge multiplicity statistics for more accurate estimation of read copy counts, and the improved use of mate pairs and min-cost flow for supporting edge merging. The assemblies produced by SAGE for several short and medium-size genomes compared favourably with those of existing leading assemblers.

3. FSG: Fast String Graph

The new integrated assembler has been assessed on a standard benchmark, showing that fast string graph (FSG) is significantly faster than SGA while maintaining a moderate use of main memory, and showing practical advantages in running FSG on multiple threads. Moreover, we have studied the effect of coverage rates on the running times.

4.  BASE https://github.com/dhlbh/BASE

It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs. BASE is a practically efficient tool for constructing contig, with significant improvement in quality for long NGS reads. It is relatively easy to extend BASE to include scaffolding.

5. Fermi https://github.com/lh3/fermi/

Fermi is a de novo assembler with a particular focus on assembling Illumina short sequence reads from a mammal-sized genome. In addition to the role of a typical assembler, fermi also aims to preserve heterozygotes which are often collapsed by other assemblers. Its ultimate goal is to find a minimal set of unitigs to represent all the information in raw reads.

If you want to learn about String Graph assembler, please read the following papers -

i) The Fragment Assembly String Graph - E. W. Myers

This paper describes the String Graph concept.

ii) Efficient construction of an assembly string graph using the FM-index - Jared T. Simpson and Richard Durbin

This earlier paper from Simpson and Durbin

iii) Efficient de novo assembly of large genomes using compressed data structures - Jared T. Simpson and Richard Durbin

y a number of metrics, including:

• Overall assembly length
• Number of scaffolds/contigs
• Length of longest scaffold/contig
• Scaffold/contig N50 and N90Assembly base composition, in particular percentage GC and percentage Ns
• CEGMA completeness
• Scaffold/contig length/count distribution

assembly-stats supports two widely used presentations of these values, tabular and cumulative length plots, and introduces an additional circular plot that summarises most commonly used assembly metrics in a single visualisation. Each of these presentations is generated using javascript from a common (JSON) data structure, allowing toggling between alternative views, and each can be applied to a single or multiple assemblies to allow direct comparison of alternate assemblies.

Tabular presentation allows direct comparison of exact values between assemblies, the limitations of this approach lie in the necessary omission of distributions and the challenge of interpreting ratios of values that may vary by several orders of magnitude.

Address of the bookmark: https://github.com/rjchallis/assembly-stats