Results for "Variant"
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Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version 3.3. Genome Analysis Toolkit 0...Tags: Best, Practices, Variant, Calling, GATK
1527 days ago
QuasiModo - Quasispecies Metric Determination on Omics
This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each consisting of two lab strains in different abundance ra...Tags: QuasiModo, Quasispecies, Metric, Determination, Omics, Virus, Genome, Variant, Assembly, SNP
1036 days ago
Calling variants in non-diploid systems
The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA a...Tags: Variant, Prokaryotic, virus, genome, snp, tutorial, galaxy
1036 days ago
Classification of SARS-CoV2 Variant !
The scientists established some guidelines for determining whether a variant is a legitimate branch of an existing lineage: The variant should be transmitted from its original location to another "geographically distinct population"—say, another country or a province of a large and populou...Tags: SARS-CoV2, Variant, Classification, Lineage
883 days ago
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 tha...Tags: DAVI, deep, alignment, variant, identification, tool, snp
1139 days ago
AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to conventional public pipelines and ∼48% to the in-hou...Tags: AIRVF, filtering, toolbox, precise, variant, calling, Ion, Torrent, sequencing
2319 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a cons...Tags: Snippy, Rapid, haploid, variant, calling, core, SNP, phylogeny, bacteria
2017 days ago
