<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/42017?offset=50 https://bioinformaticsonline.com/bookmarks/view/33011/grinder-biogrinder-a-versatile-omics-shotgun-and-amplicon-sequencing-read-simulator Wed, 24 May 2017 08:41:41 -0500 https://bioinformaticsonline.com/bookmarks/view/33011/grinder-biogrinder-a-versatile-omics-shotgun-and-amplicon-sequencing-read-simulator <![CDATA[Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator]]> Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file.

Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced.

Address of the bookmark: https://sourceforge.net/projects/biogrinder/files/biogrinder/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35543/genometools-the-versatile-open-source-genome-analysis-software Wed, 07 Feb 2018 10:44:18 -0600 https://bioinformaticsonline.com/bookmarks/view/35543/genometools-the-versatile-open-source-genome-analysis-software <![CDATA[GenomeTools: The versatile open source genome analysis software]]> The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.

If you are interested in gene prediction, have a look at GenomeThreader.

Address of the bookmark: http://genometools.org/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41875/virtualflow-a-versatile-parallel-workflow-platform-for-carrying-out-virtual-screening Sat, 13 Jun 2020 13:03:09 -0500 https://bioinformaticsonline.com/bookmarks/view/41875/virtualflow-a-versatile-parallel-workflow-platform-for-carrying-out-virtual-screening <![CDATA[VirtualFlow: a versatile, parallel workflow platform for carrying out virtual screening]]>  related tasks on Linux-based computer clusters of any type and size which are managed by a batchsystem (such as SLURM). 

Currently, there exist two versions of VirtualFlow, which are tailored to different types of tasks:

They use the same core technology regarding the workflow management and parallelization, and they can be used individually or in concert with each other. Additional versions are expected to arrive in the future. 

https://github.com/VirtualFlow

https://www.nature.com/articles/s41586-020-2117-z?

Address of the bookmark: https://virtual-flow.org/

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