<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36880?offset=120 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/27847/anvio Thu, 16 Jun 2016 18:15:41 -0500 https://bioinformaticsonline.com/bookmarks/view/27847/anvio <![CDATA[Anvio]]> In a nutshell

Anvi’o is an analysis and visualization platform for ‘omics data.

Please find the methods paper here: https://peerj.com/articles/1319/

Anvi’o would not have been possible without the help of many people who directly or indirectly contributed to its development. Here is the acknowledgements section of our methods paper

An analysis and visualization platform for 'omics data http://merenlab.org/projects/anvio

Paper https://peerj.com/articles/1839/

Address of the bookmark: https://github.com/meren/anvio

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/28117/quin%E2%80%99s-web-server Mon, 27 Jun 2016 10:44:16 -0500 https://bioinformaticsonline.com/bookmarks/view/28117/quin%E2%80%99s-web-server <![CDATA[QuIN’s web server]]> Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. 

AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub:https://github.com/UcarLab/QuIN/.

Address of the bookmark: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004809

]]> Jit https://bioinformaticsonline.com/news/view/28199/genome-workbench-2107 Fri, 01 Jul 2016 12:09:59 -0500 https://bioinformaticsonline.com/news/view/28199/genome-workbench-2107 <![CDATA[Genome Workbench 2.10.7]]> Genome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.

For the full list of features, improvements and fixes, see the release notes:https://ncbi.nlm.nih.gov/tools/gbench/releasenotes

New Features

  • BLAST Tool: added support for local custom BLAST databases
  • Graphical Sequence View: added log scaling option for graph tracks
  • Generic Table View: new tutorial added

Bug Fixes and Improvements

  • Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
  • Tree View: layout updated to better accommodate nodes of different sizes
  • Table Import Dialog (MacOS): fixed issue with table visibility
  • Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
  • Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
  • Graphical Sequence View: fixed protein coloration methods
  • Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
  • Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
  • Search View: ORF Finder – fixed incorrect protein lengths
  • Fixed bug with not opening project file (.gbp) on a click
  • Fixed issues in GVF import
  • Fixed BLAST Search tool against NCBI databases not working
  • Fixed tblastn (protein BLAST) not working in standalone mode
  • Fixed GTF export failure
]]> Gudiya Pal https://bioinformaticsonline.com/bookmarks/view/28290/bioinformatics-tools-and-software Tue, 05 Jul 2016 10:02:26 -0500 https://bioinformaticsonline.com/bookmarks/view/28290/bioinformatics-tools-and-software <![CDATA[Bioinformatics tools and software]]> USEARCH >
Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >
Multiple sequence alignment. Faster and more accurate than CLUSTALW.

 UPARSE >
OTU clustering for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures. UCHIME >
Chimeric sequence detection. PILER >
De novo genome repeat finder. PILER-CR >
Detection of CRISPR repeats in bacterial genomes. QSCORE >
Compare two multiple alignments for benchmarking. PALS >
Whole-genome alignment. PREFAB >
Protein Reference Alignment Database. MSA benchmark collection >
Selected multiple alignment benchmarks in a standardized FASTA format.

Address of the bookmark: http://drive5.com/software.html

]]> 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/29276/murasaki Fri, 30 Sep 2016 10:22:30 -0500 https://bioinformaticsonline.com/bookmarks/view/29276/murasaki <![CDATA[Murasaki]]> Murasaki is an anchor alignment program that is

  • exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 35 wall minutes), or 8 mammals in 21 CPU hours (42 wall minutes))
  • scalable (Arbitrarily parallelizable across multiple nodes using MPI)
  • memory efficient. (Even a single node with 16GB of ram can handle over 1Gbp of sequence)
  • unlimited by pattern length or selection
  • repeat tolerant

image

Address of the bookmark: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?Murasaki

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/29305/miro-mirna-omics Tue, 04 Oct 2016 14:50:48 -0500 https://bioinformaticsonline.com/bookmarks/view/29305/miro-mirna-omics <![CDATA[MIRO : miRNA omics]]> The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of reads generated with the Illumina sequencing platform. MIRO allows to preprocess the Solexa-reads, map them flexibly to several reference genomes using one of four different mappers, create differential gene (miRNA) expression profiles and cluster reads using one of several algorithm. MIRO output is furthermore compatible with software such as genome browsers and miRDeep.

Address of the bookmark: http://seq.crg.es/download/software/Miro/

]]> Jit https://bioinformaticsonline.com/file/view/29601/statistics-using-r-with-biological-examples Thu, 03 Nov 2016 04:55:41 -0500 https://bioinformaticsonline.com/file/view/29601/statistics-using-r-with-biological-examples <![CDATA[Statistics Using R with Biological Examples]]> This book is a manifestation of my desire to teach researchers in biology a bit more about statistics than an ordinary introductory course covers and to introduce the utilization of R as a tool for analyzing their data. My goal is to reach those with little or no training in higher level statistics so that they can do more of their own data analysis, communicate more with statisticians, and appreciate the great potential statistics has to offer as a tool to answer biological questions.

This is necessary in light of the increasing use of higher level statistics in biomedical research. I hope it accomplishes this mission and encourage its free distribution and use as a course text or supplement.

K Seefeld, May 2007

]]> Neel https://bioinformaticsonline.com/bookmarks/view/30012/swalo Wed, 30 Nov 2016 05:06:05 -0600 https://bioinformaticsonline.com/bookmarks/view/30012/swalo <![CDATA[SWALO]]> SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing.

Download

Git repository of SWALO is at https://github.com/atifrahman/SWALO.

Address of the bookmark: https://atifrahman.github.io/SWALO/

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