<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36755?offset=150 https://bioinformaticsonline.com/bookmarks/view/27463/bpipe-a-tool-for-running-and-managing-bioinformatics-pipelines Sat, 21 May 2016 22:42:16 -0500 https://bioinformaticsonline.com/bookmarks/view/27463/bpipe-a-tool-for-running-and-managing-bioinformatics-pipelines <![CDATA[Bpipe - a tool for running and managing bioinformatics pipelines]]> Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'.

Bpipe has been published in Bioinformatics! If you use Bpipe, please cite:

Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics

Address of the bookmark: http://docs.bpipe.org/

]]> Radha Agarkar https://bioinformaticsonline.com/bookmarks/view/30680/easybuild Fri, 27 Jan 2017 16:00:43 -0600 https://bioinformaticsonline.com/bookmarks/view/30680/easybuild <![CDATA[EasyBuild]]> EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
A full list of supported software packages is available here.

Address of the bookmark: https://hpcugent.github.io/easybuild/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34678/svfinder-tool-for-detecting-genomic-rearrangement-form-dna-seq-data Thu, 14 Dec 2017 15:51:40 -0600 https://bioinformaticsonline.com/bookmarks/view/34678/svfinder-tool-for-detecting-genomic-rearrangement-form-dna-seq-data <![CDATA[SVfinder: Tool for detecting genomic rearrangement form DNA-seq data]]> SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

Address of the bookmark: https://github.com/cauyrd/SVfinder

]]> Robert M Willioms https://bioinformaticsonline.com/bookmarks/view/36012/gmol-an-interactive-tool-for-3d-genome-structure-visualization Wed, 21 Mar 2018 12:25:20 -0500 https://bioinformaticsonline.com/bookmarks/view/36012/gmol-an-interactive-tool-for-3d-genome-structure-visualization <![CDATA[GMOL: An Interactive Tool for 3D Genome Structure Visualization]]> GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.

Address of the bookmark: https://www.nature.com/articles/srep20802

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42204/g-nest-the-gene-neighborhood-scoring-tool Fri, 25 Sep 2020 20:09:18 -0500 https://bioinformaticsonline.com/bookmarks/view/42204/g-nest-the-gene-neighborhood-scoring-tool <![CDATA[G-NEST: The Gene NEighborhood Scoring Tool]]> The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin. Example data files are in the separate repository.

Address of the bookmark: https://github.com/dglemay/G-NEST

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44659/figeno-tool-for-plotting-sequencing-data-along-genomic-coordinates Tue, 17 Sep 2024 02:28:15 -0500 https://bioinformaticsonline.com/bookmarks/view/44659/figeno-tool-for-plotting-sequencing-data-along-genomic-coordinates <![CDATA[Figeno: Tool for plotting sequencing data along genomic coordinates.]]> Tool for plotting sequencing data along genomic coordinates.

FIGENO is a
  FIGure
    GENerator
for GENOmics

With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview: https://www.youtube.com/watch?v=h1cBeXoSYTA.

figeno

Address of the bookmark: https://github.com/CompEpigen/figeno

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/33693/circleator Sun, 25 Jun 2017 18:04:32 -0500 https://bioinformaticsonline.com/bookmarks/view/33693/circleator <![CDATA[Circleator]]> The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:

Sample Circleator image

Common uses of the tool include:

  • Displaying the sequence and/or genes in a GenBank flat file.
  • Highlighting differences and/or similarities in gene content between related organisms.
  • Comparing SNPs and indels between closely-related strains or serovars.
  • Comparing gene expression values across multiple samples or timepoints.
  • Visualizing coverage plots of RNA-Seq read alignments.

Key Features

Circleator...

  • Builds on BioPerl and the input file formats that it supports, including:
  • Accepts a number of other commonly-used datatypes and file formats:
    • BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
  • Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
  • Requires only a single configuration file whose layout mirrors that of the figure itself.
    • Predefined configuration files and "track" types are supplied for common datasets.
    • Advanced features allow limited analyses to be performed as a figure is drawn.
  • Includes an extensive set of regression tests.
  • Offers a prototype web-based GUI (under the "Ringmaster" project.)

https://github.com/jonathancrabtree/Circleator

Address of the bookmark: https://github.com/jonathancrabtree/Circleator

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34567/jobtree-based-python-wrapper-to-run-the-genome-simulation-tool-suite-evolver Fri, 08 Dec 2017 16:26:32 -0600 https://bioinformaticsonline.com/bookmarks/view/34567/jobtree-based-python-wrapper-to-run-the-genome-simulation-tool-suite-evolver <![CDATA[jobTree based python wrapper to run the genome simulation tool suite Evolver]]> evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also included are convenience scripts to: check on a running simulation and see detailed status and logging information; extract fasta sequence files from the leaf nodes of a completed simulation; extract pairwise multiple alignment files (.maf) from leaf and branch nodes from a completed simulation and with the help of mafJoin, join them together into a single maf covering the entire simulation.

Address of the bookmark: https://github.com/dentearl/evolverSimControl

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35249/gpopsim-a-simulation-tool-for-whole-genome-genetic-data Wed, 17 Jan 2018 03:47:46 -0600 https://bioinformaticsonline.com/bookmarks/view/35249/gpopsim-a-simulation-tool-for-whole-genome-genetic-data <![CDATA[GPOPSIM: a simulation tool for whole-genome genetic data]]> GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can simulate multiple genetically correlated traits with desired genetic parameters and underlying genetic architectures.

Address of the bookmark: https://github.com/SCAU-AnimalGenetics/GPOPSIM

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36857/%E2%80%9Cone-code-to-find-them-all%E2%80%9D-a-perl-tool-to-conveniently-parse-repeatmasker-output-files Mon, 04 Jun 2018 03:45:15 -0500 https://bioinformaticsonline.com/bookmarks/view/36857/%E2%80%9Cone-code-to-find-them-all%E2%80%9D-a-perl-tool-to-conveniently-parse-repeatmasker-output-files <![CDATA[“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files]]> Address of the bookmark: http://doua.prabi.fr/software/one-code-to-find-them-all

]]> Poonam Mahapatra