<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/39383?offset=60 https://bioinformaticsonline.com/bookmarks/view/42963/davi-deep-learning-based-tool-for-alignment-and-single-nucleotide-variant-identification Tue, 16 Mar 2021 05:41:33 -0500 https://bioinformaticsonline.com/bookmarks/view/42963/davi-deep-learning-based-tool-for-alignment-and-single-nucleotide-variant-identification <![CDATA[DAVI: Deep learning-based tool for alignment and single nucleotide variant identification]]> DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can be used across different NGS technologies as well as across different species

https://iopscience.iop.org/article/10.1088/2632-2153/ab7e19/pdf

Address of the bookmark: https://github.com/gguptaiitd/NEAT

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40699/kevler-reference-free-variant-discovery-in-large-eukaryotic-genomes Tue, 28 Jan 2020 03:21:53 -0600 https://bioinformaticsonline.com/bookmarks/view/40699/kevler-reference-free-variant-discovery-in-large-eukaryotic-genomes <![CDATA[Kevler: Reference-free variant discovery in large eukaryotic genomes]]> Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs), insertion/deletion variants (indels), and structural variants (SVs) simultaneously with a single simple model. 

More at https://kevlar.readthedocs.io/en/latest/

https://www.cell.com/iscience/pdf/S2589-0042(19)30259-7.pdf

Address of the bookmark: https://github.com/kevlar-dev/kevlar

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41916/truvari-structural-variant-comparison-tool-for-vcfs Tue, 30 Jun 2020 21:30:44 -0500 https://bioinformaticsonline.com/bookmarks/view/41916/truvari-structural-variant-comparison-tool-for-vcfs <![CDATA[truvari: Structural variant comparison tool for VCFs]]> Structural variant comparison tool for VCFs

Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure.

Spiral Genetics

Motivation

Address of the bookmark: https://github.com/spiralgenetics/truvari

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44501/minda-a-tool-for-evaluating-structural-variant-sv-callers Sun, 31 Mar 2024 02:43:50 -0500 https://bioinformaticsonline.com/bookmarks/view/44501/minda-a-tool-for-evaluating-structural-variant-sv-callers <![CDATA[Minda: a tool for evaluating structural variant (SV) callers]]> Minda is a tool for evaluating structural variant (SV) callers that

  • standardizes VCF records for compatibility with both germline and somatic SV callers,
  • benchmarks against a single VCF input file, or
  • benchmarks against an ensemble call set created from multiple VCF input files.

Address of the bookmark: https://github.com/KolmogorovLab/minda

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