<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/42559?offset=20 https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases Wed, 12 Feb 2020 01:16:29 -0600 https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases <![CDATA[Biological databases !]]> Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

]]> BioStar https://bioinformaticsonline.com/blog/view/36525/installing-bandage-on-ubunty Tue, 08 May 2018 08:03:21 -0500 https://bioinformaticsonline.com/blog/view/36525/installing-bandage-on-ubunty <![CDATA[Installing Bandage on Ubunty !]]> The following instructions successfully build Bandage (https://github.com/rrwick/Bandage ) on a fresh installation of Ubuntu 14.04:

  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
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Hit:3 http://ppa.launchpad.net/webupd8team/java/ubuntu xenial InRelease 
Hit:4 http://be.archive.ubuntu.com/ubuntu xenial InRelease 
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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]
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Get:14 http://security.ubuntu.com/ubuntu xenial-security/main Translation-en [209 kB]
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Get:17 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 DEP-11 Metadata [107 kB]
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Get:21 http://be.archive.ubuntu.com/ubuntu xenial-updates/main Translation-en [319 kB]
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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
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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
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Get:3 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5network5 amd64 5.5.1+dfsg-16ubuntu7.5 [540 kB]
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Get:35 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libxshmfence-dev amd64 1.2-1 [3.676 B]
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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]
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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]
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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

]]> Jit https://bioinformaticsonline.com/bookmarks/view/31100/vaguevelvet-assembler-graphical-front-end Fri, 24 Feb 2017 08:56:49 -0600 https://bioinformaticsonline.com/bookmarks/view/31100/vaguevelvet-assembler-graphical-front-end <![CDATA[VAGUE:Velvet Assembler Graphical Front End]]> VAGUE is a vague acronym for "Velvet Assembler Graphical Front End", which means it is a GUI for the Velvet de novo assembler. The command line version of Velvet can be complicated for beginners to use, but VAGUE makes it clear and simple

More at http://www.vicbioinformatics.com/software.vague.shtml

Address of the bookmark: http://www.vicbioinformatics.com/software.vague.shtml

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29130/gage-genome-assembly-gold-standard-evaluation Wed, 07 Sep 2016 07:35:49 -0500 https://bioinformaticsonline.com/bookmarks/view/29130/gage-genome-assembly-gold-standard-evaluation <![CDATA[GAGE : Genome Assembly Gold-standard Evaluation]]> GAGE is an evaluation of the very latest large-scale genome assembly algorithms. We have organized this "bake-off" as an attempt to produce a realistic assessment of genome assembly software in a rapidly changing field of next-generation sequencing. The main results of GAGE have now been published in the journal Genome Research: GAGE: A critical evaluation of genome assemblies and assembly algorithms.

http://genome.cshlp.org/content/early/2012/01/12/gr.131383.111

Address of the bookmark: http://gage.cbcb.umd.edu/index.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29957/record Fri, 25 Nov 2016 08:23:36 -0600 https://bioinformaticsonline.com/bookmarks/view/29957/record <![CDATA[RECORD]]> Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used. Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge. Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software.

More at https://sourceforge.net/projects/record-genome-assembler/files/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pubmed/26558255

]]> Bulbul https://bioinformaticsonline.com/bookmarks/view/30090/standardized-velvet-assembly-report Fri, 09 Dec 2016 03:59:59 -0600 https://bioinformaticsonline.com/bookmarks/view/30090/standardized-velvet-assembly-report <![CDATA[Standardized velvet assembly report]]> Requirements:

  • velvet (velveth velvetg should be in your PATH)
  • R (with Sweave)
  • pdflatex (usually part of TeTeX)
  • ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable"))
  • Perl

Optional:

  • BLAT or BLAST (to generate alignments against a reference genome). If using BLAT, add faToTwoBit,gfClient,gfServer to your PATH. If using BLAST, add blastall and formatdb.

Edit permute.sh to your liking, paying particular attention to the kmer, cvCut, expCov, and other flags

To Run:

  1. perl fastaAllSize mysequences.fa > mysequences.stat or gunzip -c mysequences.fa.gz | fastaAllSize > mysequences.stat Substitute fastqAllSize for fastq files.
  2. ./permute.sh mysequences (leave out the .fa)

https://github.com/leipzig/standardized-velvet-assembly-report

Address of the bookmark: https://github.com/leipzig/standardized-velvet-assembly-report

]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/30207/gam-ngs-genomic-assemblies-merger-for-next-generation-sequencing Mon, 19 Dec 2016 06:07:05 -0600 https://bioinformaticsonline.com/bookmarks/view/30207/gam-ngs-genomic-assemblies-merger-for-next-generation-sequencing <![CDATA[GAM-NGS: genomic assemblies merger for next generation sequencing]]> GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two assemblies representing the same genomic locus (called blocks) are identified through reads' alignments and stored in a weightedgraph. The merging phase is carried out with the help of this weighted graph that allows an optimal resolution of local problematic regions.

Address of the bookmark: https://github.com/vice87/gam-ngs

]]> Jit https://bioinformaticsonline.com/bookmarks/view/30249/genome-assembly-tutorial Tue, 20 Dec 2016 07:56:01 -0600 https://bioinformaticsonline.com/bookmarks/view/30249/genome-assembly-tutorial <![CDATA[Genome Assembly Tutorial]]> If genomes were completely random sequences in a statistical sense, 'overlap-consensus-layout' method would have been enough to assemble large genomes from Sanger reads. In contrast, real genomes often have long repetitive regions, and they are hard to assemble using overlap-consensus-layout approach. De Bruijn graph-based assembly approach was originally proposed to handle the assembly of repetitive regions better.

More at http://www.homolog.us/Tutorials/index.php?p=1.4&s=1

Address of the bookmark: http://www.homolog.us/Tutorials/index.php?p=1.4&s=1

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/31343/metabat-an-efficient-tool-for-accurately-reconstructing-single-genomes-from-complex-microbial-communities Mon, 06 Mar 2017 03:44:34 -0600 https://bioinformaticsonline.com/bookmarks/view/31343/metabat-an-efficient-tool-for-accurately-reconstructing-single-genomes-from-complex-microbial-communities <![CDATA[MetaBAT: An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities]]> MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Here we developed an automated metagenome binning software, called MetaBAT, which integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. Tested on both synthetic and real metagenome datasets, MetaBAT outperforms alternative methods in both accuracy and computational efficiency. Applying MetaBAT to an assembly from 1,704 human gut samples formed 1,634 genome bins (>200kb) in 3 hours, where 621 genome bins are >50% complete with <5% contamination from other species. Further analysis shows that the quality of these genome bins approaches manually curated genomes.

Address of the bookmark: https://bitbucket.org/berkeleylab/metabat

]]> Jit https://bioinformaticsonline.com/bookmarks/view/31105/understanding-pacbio Fri, 24 Feb 2017 10:17:36 -0600 https://bioinformaticsonline.com/bookmarks/view/31105/understanding-pacbio <![CDATA[Understanding PacBio]]> This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you get started with your data processing, as well as information for specialized applications.

Training Resources:

Specialized Applications:

Address of the bookmark: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki

]]> Jitendra Narayan