<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38475?offset=240 https://bioinformaticsonline.com/bookmarks/view/36478/the-marvel-assembler Fri, 04 May 2018 19:18:41 -0500 https://bioinformaticsonline.com/bookmarks/view/36478/the-marvel-assembler <![CDATA[The MARVEL assembler]]> MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.

The assembly process can be summarized as follows:

  1. overlap
  2. patch reads
  3. overlap (again)
  4. scrubbing
  5. assembly graph construction and touring
  6. optional read correction
  7. fasta file creation

Address of the bookmark: https://github.com/schloi/MARVEL

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36597/gappadder-a-sensitive-approach-for-closing-gaps-on-draft-genomes-with-short-sequence-reads Mon, 14 May 2018 05:25:48 -0500 https://bioinformaticsonline.com/bookmarks/view/36597/gappadder-a-sensitive-approach-for-closing-gaps-on-draft-genomes-with-short-sequence-reads <![CDATA[GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads]]> This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this documentation, is distributed free of charge. If you use this program in a publication, please cite the following reference:
Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads." bioRxiv (2017): 125534.

Address of the bookmark: https://github.com/Reedwarbler/GAPPadder

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37257/asar-advanced-metagenomic-sequence-analysis-in-r Mon, 09 Jul 2018 05:20:50 -0500 https://bioinformaticsonline.com/bookmarks/view/37257/asar-advanced-metagenomic-sequence-analysis-in-r <![CDATA[ASAR: Advanced metagenomic Sequence Analysis in R]]> An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37984/baum-%E2%80%93-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus Wed, 24 Oct 2018 23:35:09 -0500 https://bioinformaticsonline.com/bookmarks/view/37984/baum-%E2%80%93-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus <![CDATA[BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus]]> BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the results of existing assemblies that are obtained based on short or long sequencing reads. 

Address of the bookmark: http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38316/simba-a-genome-assembly-project-management-system Thu, 29 Nov 2018 08:52:25 -0600 https://bioinformaticsonline.com/bookmarks/view/38316/simba-a-genome-assembly-project-management-system <![CDATA[SIMBA: a Genome Assembly Project Management System]]> SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

Address of the bookmark: http://ufmg-simba.sourceforge.net/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/38668/gvolante-completeness-assessment-of-genometranscriptome-sequences Sun, 13 Jan 2019 07:03:25 -0600 https://bioinformaticsonline.com/bookmarks/view/38668/gvolante-completeness-assessment-of-genometranscriptome-sequences <![CDATA[gVolante: Completeness Assessment of Genome/Transcriptome Sequences]]> A brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section

Address of the bookmark: https://gvolante.riken.jp/analysis.html

]]> Neel https://bioinformaticsonline.com/news/view/39217/caulobacter-ethensis-20-computer-generated-genome-of-a-living-organism Wed, 03 Apr 2019 08:45:22 -0500 https://bioinformaticsonline.com/news/view/39217/caulobacter-ethensis-20-computer-generated-genome-of-a-living-organism <![CDATA[Caulobacter ethensis - 2.0 : Computer-generated Genome of a Living Organism]]> All the genome sequences of organisms known throughout the world are stored in a database belonging to the National Center for Biotechnology Information in the United States. As of today, the database has an additional entry: Caulobacter ethensis-2.0. 
 
It is the world's first fully computer-generated genome of a living organism, developed by scientists at ETH Zurich. 
 
However, it must be emphasised that although the genome for C. ethensis-2.0 was physically produced in the form of a very large DNA molecule, a corresponding organism does not yet exist.
 
]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/39821/gvolante-completeness-assessment-of-genometranscriptome-sequences Tue, 06 Aug 2019 21:37:56 -0500 https://bioinformaticsonline.com/bookmarks/view/39821/gvolante-completeness-assessment-of-genometranscriptome-sequences <![CDATA[gVolante: Completeness Assessment of Genome/Transcriptome Sequences]]> gVolante provides an online interface for completeness assessment of user’s original or publicly available sequence datasets as well as for browsing results of completeness assessment performed on publicly available genome and transcriptome assemblies.

image

Address of the bookmark: https://gvolante.riken.jp/

]]> Jit https://bioinformaticsonline.com/researchlabs/view/40609/genome-informatics-section-lab Sat, 25 Jan 2020 06:38:23 -0600 <![CDATA[Genome Informatics Section Lab !]]> Our section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. We aim to improve such foundational processes and translate emerging genomic technologies into practice.

The Genome Informatics Section is hiring! Come join our outstanding team at the NIH’s National Human Genome Research Institute and contribute to the development of new reference genomes and computational methods for DNA sequencing and analysis. Both postdoc and PhD students positions are available. More information and application instructions follow below.

More at https://genomeinformatics.github.io/

]]> 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