<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/42936?offset=70 https://bioinformaticsonline.com/bookmarks/view/44311/jbrowse-2-a-modular-genome-browser-with-views-of-synteny-and-structural-variation Tue, 25 Apr 2023 20:58:52 -0500 https://bioinformaticsonline.com/bookmarks/view/44311/jbrowse-2-a-modular-genome-browser-with-views-of-synteny-and-structural-variation <![CDATA[JBrowse 2: a modular genome browser with views of synteny and structural variation]]>
  • igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests)
  • jb2-web - stock instance of jbrowse-web v1.7.5
  • jb1 - stock instance of jbrowse 1 v1.16.11
  • jb2 embedded - a create-react-app with @jbrowse/react-linear-genome-view

    • Address of the bookmark: https://github.com/GMOD/jb2profile

    ]]>     Abhi     https://bioinformaticsonline.com/pages/view/44377/mitochondrial-genome-assembly-tools Wed, 06 Sep 2023 00:37:18 -0500 https://bioinformaticsonline.com/pages/view/44377/mitochondrial-genome-assembly-tools <![CDATA[Mitochondrial genome assembly tools !]]> Mitochondrial genome assembly tools are specialized software and algorithms designed to accurately reconstruct the mitochondrial genome (mitogenome) from sequencing data, typically obtained through techniques like next-generation sequencing (NGS). The mitochondrial genome is relatively small compared to the nuclear genome, making it an ideal target for assembly. Here are some commonly used mitochondrial genome assembly tools:

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

    MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

    MITObim: MITObim is a tool specifically developed for the iterative assembly of mitochondrial genomes. It starts with a reference mitogenome and iteratively refines the assembly using the read data.

    MITOS: MITOS is a web-based platform that provides a pipeline for annotating mitochondrial genomes. It integrates multiple software tools for assembly, annotation, and visualization of mitogenomes.

    MIRA: MIRA (Mimicking Intelligent Read Assembly) is a versatile genome assembly tool that can be used for mitochondrial genome assembly. It supports various sequencing technologies and allows for reference-based or de novo assembly.

    NOVOPlasty: NOVOPlasty is a user-friendly tool designed for de novo assembly of organelle genomes, including mitochondria. It utilizes a seed-and-extend algorithm and is suitable for both short-read and long-read data.

    MITOS2: MITOS2 is an updated version of the MITOS pipeline, which automates the annotation of mitochondrial genomes. It provides improved accuracy and additional features for mitochondrial genome analysis.

    GetOrganelle: While primarily designed for chloroplast genome assembly, GetOrganelle can also be used for mitochondrial genome assembly. It is particularly useful for dealing with high-throughput sequencing data.

    SPAdes: SPAdes (St. Petersburg genome assembler) is a versatile genome assembly tool that can be employed for mitochondrial genome assembly, especially when dealing with complex datasets that may contain nuclear mitochondrial DNA sequences (numts).

    IDBA-UD: IDBA-UD (Iterative De Bruijn Graph De Novo Assembler) is another de novo assembly tool that can be used for mitochondrial genome assembly, especially in cases with relatively low coverage.

    Velvet: Velvet is a de novo assembly tool that can be applied to mitochondrial genome assembly, especially when working with short-read data.

    When selecting a mitochondrial genome assembly tool, it's important to consider the specific characteristics of your sequencing data, such as read length and coverage, as well as the complexity of the mitochondrial genome. Additionally, some tools are better suited for specific organisms or research objectives, so choosing the right tool will depend on your particular project requirements.

    ]]>     Abhi     https://bioinformaticsonline.com/blog/view/4574/tools-to-detect-synteny-blocks-regions-among-multiple-genomes Mon, 16 Sep 2013 17:12:02 -0500 https://bioinformaticsonline.com/blog/view/4574/tools-to-detect-synteny-blocks-regions-among-multiple-genomes <![CDATA[Tools to detect synteny blocks regions among multiple genomes]]> The synteny block (which etymologically means “on the same ribbon”) is a collection of contiguous genes located on the same chromosome. These block regions have mostly been preserved by genome rearrangements, and so synteny blocks from two related species (e.g., humans and mice) will be roughly similar but flipped around on the respective genomes. Ovcharenko et. al. define it as ‘any conserved sequence blocks, regardless of whether it encompasses multiple genes, an area containing single genes, or areas devoid of known genes to be considers as synteny block as long as there is conservation at the sequence level. Today, however, biologists usually refer to synteny as the conservation of blocks of order within two sets of chromosomes that are being compared with each other. This concept can also be referred to as shared synteny. The NHBLI/NCBI Glossary define synteny as “Two genes which occur on the same chromosome are syntenic; however, syntenic genes may or may not be "linked."

    Now a day, geneticists have developed a language of their own. They are pouring lots of money and energy to read the entire genomic text and understand the gods own code ATGC. It is somewhat fascinating, not only for geneticist but also for non-biologist to know that there are several conserved blocks in genome which remain conserved over hundreds of millions of years. There have been several researches on conserved blocks and non-conserved regions to understand the mechanism and importance of all these regions (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675965/). The finding indicates conservation and rearrangements of certain evolutionary important genes play an important role in evolution/adaptive changes (http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html https://academic.oup.com/gbe/article/8/8/2442/2198198/Novel-Insights-into-Chromosome-Evolution-in-Birds , http://science.sciencemag.org/content/346/6215/1311).

    But the puzzle remains open, how to correctly define the synteny (presence of two or more genes on the same chromosome) and conserved synteny (presence of two or more genes on chromosome of each of the two species) on several genomes.

    image

    Figure: Image generated with Evolution Highway (EH) tool http://eh-demo.ncsa.illinois.edu/ 

    Keeping the new approach to define conserved synteny in mind there have been various algorithms developed to identify the conserved homologous synteny blocks (HSB) amongst species. Some of them which were commonly used for synteny detections are:

    SyntenyTracker ( http://www-app.igb.uiuc.edu/labs/lewin/donthu/Synteny_assign/html/),

    SyntenyTracker was shown to be an efficient and accurate automated tool for defining HSBs using datasets that may contain minor errors resulting from limitations in map construction methodologies.

    CoGe (http://genomevolution.org/CoGe/SynFind.pl )

    Satsuma (http://evomics.org/learning/genomics/satsuma/)

    Cinteny (http://cinteny.cchmc.org/) ,

    Cinteny server can be used for finding regions syntenic across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure.

    OrthoCluster (http://krono.act.uji.es/noticias/orthocluster-a-new-tool-for-mining-syntenic-blocks)

    A new tool for mining syntenic blocks in comparative genomics

    SynMap (http://genomevolution.org/wiki/index.php/SynMap),

    SyMAP (http://www.symapdb.org/)

    SyMAP (Synteny Mapping and Analysis Program) v4.0 is an automated system for identifying and displaying genome synteny alignments. The genomes may be represented by sequenced chromosomes (pseudomolecules), by draft sequence contigs, or by FPC physical maps (with BAC-end or marker sequence).

    http://genomevolution.org/CoGe/SynMap.pl

    RegionMiner (http://www.genomatix.de/online_help/help_regionminer/orthologous.html)

    SyntenyMiner is being developed as an application to visualize and interrogate comparisons among multiple complete genome sequences. http://syntenyminer.sourceforge.net/

    AutoGRAPH ( http://autograph.genouest.org/),

    AutoGRAPH is an integrated web server for multi-species comparative genomic analysis. It is designed for constructing and visualizing synteny maps between two or three species, determination and display of macrosynteny and microsynteny relationships among species, and for highlighting evolutionary breakpoints.

    SynChro(http://www.lgm.upmc.fr/CHROnicle/SynChro.html)

    SynChro is a tool designed to define conserved synteny blocks. It reconstructs synteny blocks between pairwise comparison of multiple genomes. The reconstructed synteny blocks may overlap each other, be included in one another or duplicated due to micro-rearrangements.

    SyntenyView ( http://www.cbs.dtu.dk/dtucourse/cookbooks/nikob/exercises/gf1_output_5.html),

    Ensembl 'SyntenyView' shows conservation of large-scale gene order between species pairs. A brief summary of the calculation method appears at the bottom of this help page.  The left of a 'SyntenyView' page displays a diagram of chromosomes with blocks of conserved synteny. The right of a page shows homology matches between individual genes within syntenic blocks.

    SynBrowse ( http://www.synbrowse.org/),

    SynBrowse (Synteny Browser) is a generic sequence comparison tool for visualizing genome alignments both within and between species. It is intended to help scientists study and analyze synteny, homologous genes and other conserved elements between sequences. This software is useful in studying genome duplication and evolution. It can also aid in identifying uncharacterized genes, putative regulatory elements and novel structural features of study species by comparing to a well annotated reference sequence, thus enabling genome curators to refine and edit annotations of species that have incomplete genome annotations.

    Sibelia (http://arxiv.org/abs/1307.7941).

    A comparative genomic tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.

    GSV (http://cas-bioinfo.cas.unt.edu/gsv/homepage.php)

    Genome Synteny Viewer allows users to upload files which contain synteny regions between two or more genomes and interactively visualize the synteny between them. GSV also allows users to upload annotation files to visualize annotated regions in addition to synteny regions.

    MicroSyn (http://www.lgm.upmc.fr/CHROnicle/SynChro.html)

    MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family.

    SynOrth (http://synorth.genereg.net/)

    Synorth [s n ôrth], named in combination of "synteny" and "ortholog", is designed for the study of evolutionary changes of genomic regulatory blocks (GRBs) in vertebrate genomes, and especially the changes following the whole-genome duplication in teleost fish, by tracing the ortholog genes gain and loss in ancient synteny blocks.

    SyDiG (http://www.ncbi.nlm.nih.gov/pubmed/21441096)

    Uncovering Synteny in Distant Genomes.

    MapSynteny  (http://www.automatizacionysistemas.com/download.html)

    MapSynteny is a macro in MS Excel® able to create images to show the relationship between genetic maps and large sequences (scaffolds, chromosomes, BACs, etc.). Based on tab – delimited BLAST results and some formulas, a suitable image of syntenic relationships or physical mapping can be obtained. http://www.automatizacionysistemas.com/Poster_MapSynteny.pdf

    One of the best synteny tutorial for beginer @ http://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-genomes-44022

    Reference:

    http://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-genomes-44022

    http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html

    http://en.wikipedia.org/wiki/Synteny

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675965/

    ]]>     Jitendra Narayan     https://bioinformaticsonline.com/news/view/19090/deeptools Sat, 08 Nov 2014 15:02:08 -0600 https://bioinformaticsonline.com/news/view/19090/deeptools <![CDATA[deepTools]]> deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allows the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.

    Publicaton: http://nar.oxfordjournals.org/content/early/2014/05/05/nar.gku365.full

    Source Code and Wiki: https://github.com/fidelram/deepTools/wiki

    Galaxy Tool Shed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools

    and example Galaxy workflows: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows

    ]]>     Martin Jones     https://bioinformaticsonline.com/bookmarks/view/28915/useful-bioinformatics-tools Mon, 29 Aug 2016 04:08:12 -0500 https://bioinformaticsonline.com/bookmarks/view/28915/useful-bioinformatics-tools <![CDATA[Useful Bioinformatics Tools]]> Collections of few handy tools for bioinformatician

    http://molbiol-tools.ca/Convert.htm

    Address of the bookmark: http://molbiol-tools.ca/Convert.htm

    ]]>     Poonam Mahapatra     https://bioinformaticsonline.com/bookmarks/view/30304/mcscan Thu, 22 Dec 2016 03:53:58 -0600 https://bioinformaticsonline.com/bookmarks/view/30304/mcscan <![CDATA[MCscan]]> MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences in Plant Genome Duplication Database. It is intended as an easy-to-use and quick way to identify conserved gene arrays both within the same genome and across different genomes.

    More at http://chibba.agtec.uga.edu/duplication/mcscan/

    Address of the bookmark: http://chibba.agtec.uga.edu/duplication/mcscan/

    ]]>     Bulbul     https://bioinformaticsonline.com/bookmarks/view/30550/genomering-alignment-visualization-based-on-supergenome-coordinates Wed, 18 Jan 2017 10:24:10 -0600 https://bioinformaticsonline.com/bookmarks/view/30550/genomering-alignment-visualization-based-on-supergenome-coordinates <![CDATA[GenomeRing: alignment visualization based on SuperGenome coordinates]]> The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. Such visualizations typically are either realized in a linear fashion as in genome browsers or by using a circular approach, where relationships between genomic regions are indicated by arcs. Both methods allow for the integration of additional information such as experimental data or annotations. However, providing a visualization that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supplemental data, which may be highly heterogeneous, remains a challenge.

    More at https://academic.oup.com/bioinformatics/article/28/12/i7/268598/GenomeRing-alignment-visualization-based-on

    Address of the bookmark: http://it.informatik.uni-tuebingen.de/?page_id=185

    ]]>     Neel     https://bioinformaticsonline.com/researchlabs/view/32713/salzberg-lab Mon, 15 May 2017 05:14:01 -0500 <![CDATA[Salzberg lab]]> We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with biomedical scientists to apply these methods to current problems arising in a broad spectrum of biological and medical research areas. We’re also part of the Center for Computational Biology, a group of 20+ faculty members and their labs at Johns Hopkins working on computational, statistical, and mathematical methods that can turn massive genomic data sets into biologically and clinically useful information.

    https://salzberg-lab.org/

    ]]>         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
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    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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    Setting up libxcb-xkb1:amd64 (1.11.1-1ubuntu1) ...
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    Setting up libqt5gui5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5widgets5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
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    Setting up libdrm-dev:amd64 (2.4.83-1~16.04.1) ...
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    Setting up x11proto-gl-dev (1.4.17-1) ...
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    Setting up libxext-dev:amd64 (2:1.3.3-1) ...
    Setting up x11proto-xf86vidmode-dev (2.3.1-2) ...
    Setting up libxxf86vm-dev:amd64 (1:1.1.4-1) ...
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    Setting up libxdamage-dev:amd64 (1:1.1.4-2) ...
    Setting up libxcb-glx0-dev:amd64 (1.11.1-1ubuntu1) ...
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    Setting up libxcb-dri3-dev:amd64 (1.11.1-1ubuntu1) ...
    Setting up libxcb-render0-dev:amd64 (1.11.1-1ubuntu1) ...
    Setting up libxcb-randr0-dev:amd64 (1.11.1-1ubuntu1) ...
    Setting up libxcb-shape0-dev:amd64 (1.11.1-1ubuntu1) ...
    Setting up libxcb-xfixes0-dev:amd64 (1.11.1-1ubuntu1) ...
    Setting up libxcb-sync-dev:amd64 (1.11.1-1ubuntu1) ...
    Setting up libxcb-present-dev:amd64 (1.11.1-1ubuntu1) ...
    Setting up libxshmfence-dev:amd64 (1.2-1) ...
    Setting up libx11-xcb-dev:amd64 (2:1.6.3-1ubuntu2) ...
    Setting up libwayland-bin (1.12.0-1~ubuntu16.04.3) ...
    Setting up libwayland-dev:amd64 (1.12.0-1~ubuntu16.04.3) ...
    Setting up libmircore-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
    Setting up libprotobuf9v5:amd64 (2.6.1-1.3) ...
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    Setting up libxkbcommon-dev (0.5.0-1ubuntu2) ...
    Setting up libmircommon-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
    Setting up libmircookie2:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
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    Setting up libegl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
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    Setting up mesa-common-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up libgl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up libglu1-mesa-dev:amd64 (9.0.0-2.1) ...
    Setting up libqt5concurrent5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5opengl5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5printsupport5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5sql5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5test5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5xml5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qt5-qmake:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qtbase5-dev-tools (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qtbase5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5opengl5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5sql5-sqlite:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qttranslations5-l10n (5.5.1-2build1) ...
    Processing triggers for libc-bin (2.23-0ubuntu10) ...
    ➜ 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/41604/synteny-and-rearrangement-identifier-syri Tue, 05 May 2020 10:37:10 -0500 https://bioinformaticsonline.com/bookmarks/view/41604/synteny-and-rearrangement-identifier-syri <![CDATA[Synteny and Rearrangement Identifier (SyRI)]]> SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI identifies syntenic path (longest set of co-linear regions), structural rearrangements (inversions, translocations, and duplications), local variations (SNPs, indels, CNVs etc) within syntenic and structural rearrangements, and un-aligned regions.

    Address of the bookmark: https://schneebergerlab.github.io/syri/

    ]]>     Jit