<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38819?offset=140 https://bioinformaticsonline.com/bookmarks/view/43614/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization Tue, 30 Nov 2021 23:23:57 -0600 https://bioinformaticsonline.com/bookmarks/view/43614/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization <![CDATA[MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization]]> MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads.

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44508/a-web-based-tool-for-sequence-alignment-statistics-and-innovative-visualization Thu, 04 Apr 2024 01:44:50 -0500 https://bioinformaticsonline.com/bookmarks/view/44508/a-web-based-tool-for-sequence-alignment-statistics-and-innovative-visualization <![CDATA[A web-based tool for sequence alignment statistics and innovative visualization]]> AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/

]]> BioStar https://bioinformaticsonline.com/blog/view/42974/list-of-bioinformatics-packages-for-ngs-analysis Sat, 20 Mar 2021 00:28:51 -0500 https://bioinformaticsonline.com/blog/view/42974/list-of-bioinformatics-packages-for-ngs-analysis <![CDATA[List of bioinformatics packages for NGS analysis !]]> Package suites gather software packages and installation tools for specific languages or platforms. We have some for bioinformatics software.

  • Bioconductor – A plethora of tools for analysis and comprehension of high-throughput genomic data, including 1500+ software packages. [ paper-2004 | web ]
  • Biopython – Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the Open Bioinformatics Foundation. Contains the very useful Entrez package for API access to the NCBI databases. [ paper-2009 | web ]
  • Bioconda – A channel for the conda package manager specializing in bioinformatics software. Includes a repository with 3000+ ready-to-install (with conda install) bioinformatics packages. [ paper-2018 | web ]
  • BioJulia – Bioinformatics and computational biology infastructure for the Julia programming language. [ web ]
  • Rust-Bio – Rust implementations of algorithms and data structures useful for bioinformatics. [ paper-2016 ]
  • SeqAn – The modern C++ library for sequence analysis.
]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/32853/progressivecactus Thu, 18 May 2017 05:29:29 -0500 https://bioinformaticsonline.com/bookmarks/view/32853/progressivecactus <![CDATA[progressiveCactus]]> Progressive Cactus is a whole-genome alignment package.

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

https://github.com/glennhickey/progressiveCactus

Address of the bookmark: https://github.com/glennhickey/progressiveCactus

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly Mon, 18 May 2020 16:47:56 -0500 https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly <![CDATA[Genobuntu: Package for Next Generation Sequencing and Genome Assembly]]>

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Features

  • Velvet
  • MiB
  • SSAKE
  • EULER
  • VCAKE
  • ABySS
  • ALLPATHS
  • Celera
  • SHARCGS
  • Allpaths
  • IDBA
  • TAIPAN
  • Edena
  • SOAPdenovo
  • Maq
  • IDBA-UD
  • No. of Reads present in the Ref. Seq.
  • ART NGS Reads Simulator
  • HiTEC, FASTQC
  • Minimum Description Length
  • SOAPaligner
  • Sequencing Read Archive Toolkit

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/38413/genobuntu-a-software-package-containing-more-than-70-software-and-packages-oriented-towards-ngs-and-genome-assembly Tue, 11 Dec 2018 05:15:57 -0600 https://bioinformaticsonline.com/bookmarks/view/38413/genobuntu-a-software-package-containing-more-than-70-software-and-packages-oriented-towards-ngs-and-genome-assembly <![CDATA[Genobuntu: A software package containing more than 70 software and packages oriented towards NGS and genome assembly]]> Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. 

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting. 

https://sourceforge.net/projects/genobuntu/

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/39200/omtools-a-software-package-for-visualizing-and-processing-optical-mapping-data Fri, 29 Mar 2019 01:21:54 -0500 https://bioinformaticsonline.com/bookmarks/view/39200/omtools-a-software-package-for-visualizing-and-processing-optical-mapping-data <![CDATA[OMTools: a software package for visualizing and processing optical mapping data]]> OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form an accessible and convenient pipeline for optical mapping analyses.

https://github.com/TF-Chan-Lab/OMTools

Address of the bookmark: https://github.com/TF-Chan-Lab/OMTools

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/42017/gromacs-a-versatile-package-to-perform-molecular-dynamics Thu, 06 Aug 2020 22:40:38 -0500 https://bioinformaticsonline.com/bookmarks/view/42017/gromacs-a-versatile-package-to-perform-molecular-dynamics <![CDATA[GROMACS: a versatile package to perform molecular dynamics]]> GROMACS is a versatile package to perform molecular dynamics, i.e simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is able to work with many biochemical molecules like proteins, lipids and nucleic acids. The WeNMR GROMACS web portal combines the versatility of this molecular dynamics package with the calculation power of the eNMR grid. This will enable you to perform many simulations from the comfort of your internet browser anywhere in the world. The server is furthermore aimed to provide a user friendly and efficient MD experience by performing many preparation and optimization steps automatically.

GROMACS conda https://bioconda.github.io/recipes/gromacs/README.html 

Address of the bookmark: http://haddock.science.uu.nl/enmr/services/GROMACS/main.php

]]> Neel https://bioinformaticsonline.com/bookmarks/view/43290/the-snakemake-wrappers-repository Thu, 19 Aug 2021 04:39:34 -0500 https://bioinformaticsonline.com/bookmarks/view/43290/the-snakemake-wrappers-repository <![CDATA[The Snakemake Wrappers repository]]> The Snakemake Wrapper Repository is a collection of reusable wrappers that allow to quickly use popular tools from Snakemake rules and workflows.

More at https://github.com/snakemake/snakemake-wrappers

Address of the bookmark: https://snakemake-wrappers.readthedocs.io/en/stable/

]]> BioStar https://bioinformaticsonline.com/view/119 Wed, 10 Jul 2013 14:35:34 -0500 https://bioinformaticsonline.com/view/119 <![CDATA[Which are the best statistical programming languages to study for a bioinformatician?]]> In Bio-informatics based genome sequencing and predicting metabolic pathways research jobs I used Matlab, SAS, SPSS, R and several Bioconductor packages. Matlab had a lot of powerful tools and was easy to use, whereas SPSS is for non-programmers and R need programming skills. I am wondering what other people think is best? or there might not be one specific language but a few that lend themselves best to Bio-informatics work that is math heavy and deals with a large amount of data.

]]> Jitendra Narayan