<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36405?offset=570 https://bioinformaticsonline.com/bookmarks/view/40611/deepvariant-an-analysis-pipeline-that-uses-a-deep-neural-network-to-call-genetic-variants-from-next-generation-dna-sequencing-data Sat, 25 Jan 2020 13:28:09 -0600 https://bioinformaticsonline.com/bookmarks/view/40611/deepvariant-an-analysis-pipeline-that-uses-a-deep-neural-network-to-call-genetic-variants-from-next-generation-dna-sequencing-data <![CDATA[DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.]]> DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant relies on Nucleus, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integration with the TensorFlow machine learning framework.

https://ai.googleblog.com/2017/12/deepvariant-highly-accurate-genomes.html

https://www.biorxiv.org/content/10.1101/092890v6

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Address of the bookmark: https://github.com/google/deepvariant

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41730/parliament2-runs-a-combination-of-tools-to-generate-structural-variant-calls-on-whole-genome-sequencing-data Thu, 28 May 2020 21:57:03 -0500 https://bioinformaticsonline.com/bookmarks/view/41730/parliament2-runs-a-combination-of-tools-to-generate-structural-variant-calls-on-whole-genome-sequencing-data <![CDATA[Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome sequencing data]]> Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a region, Inversions of a region, or Translocations between two regions in the genome.

Parliament2 runs a combination of tools to generate structural variant calls on whole-genome sequencing data. It can run the following callers: Breakdancer, Breakseq2, CNVnator, Delly2, Manta, and Lumpy. Because of synergies in how the programs use computational resources, these are all run in parallel. Parliament2 will produce the outputs of each of the tools for subsequent investigation.

Address of the bookmark: https://github.com/dnanexus/parliament2

]]> Jit 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

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