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Protocols

Savant specifications

Information


Unique identifier OMICS_00923
Name Savant
Alternative name Savant Genome Browser
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.0.4
Stability Stable
Maintained No

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Publications for Savant

Savant citations

 (23)
library_books

A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill

2018
Front Microbiol
PMCID: 5876298
PMID: 29628913
DOI: 10.3389/fmicb.2018.00520

[…] zation tools have also been developed in recent years, including Tablet (Milne et al., ), Integrative Genomics Viewer (IGV) (Robinson et al., ), Sequence Annotation, Visualization, and ANalysis Tool (Savant) Genome Browser (Fiume et al., ), MagicViewer (Hou et al., ), and Cytoscape (Kohl et al., ). In the microbiological studies on the DWH oil spill, these ST and databases were broadly used for an […]

library_books

Extensive RNA editing and splicing increase immune self representation diversity in medullary thymic epithelial cells

2016
Genome Biol
PMCID: 5078920
PMID: 27776542
DOI: 10.1186/s13059-016-1079-9

[…] ed from Annovar []. For this analysis we used all the reads in each sample. Adar1, Adar2, and Apobec1 normalized reads counts were calculated using DEseq []. Mapping visualization was performed using Savant genome browser []. […]

library_books

ReadXplorer 2—detailed read mapping analysis and visualization from one single source

2016
Bioinformatics
PMCID: 5167064
PMID: 27540267
DOI: 10.1093/bioinformatics/btw541

[…] S4 that ReadXplorer 2 offers several unique features and combines many useful features that are not present in this composition in one of the other commonly used read mapping visualization tools like Savant (), Integrated Genome Browser (IGB) (), Artemis (), Integrative Genomics Viewer (IGV) () and GenomeView ().Finally, we assessed the performance of analysis functions offered by ReadXplorer 2. W […]

library_books

A survey of best practices for RNA seq data analysis

2016
Genome Biol
PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] p), unnormalized (for example, total count) or normalized, using genome browsers such as the UCSC browser [], Integrative Genomics Viewer (IGV) [] (Figure S1a in Additional file ), Genome Maps [], or Savant []. Some visualization tools are specifically designed for visualizing multiple RNA-seq samples, such as RNAseqViewer [], which provides flexible ways to display the read abundances on exons, t […]

call_split

Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation

2015
PLoS Pathog
PMCID: 4654494
PMID: 26588216
DOI: 10.1371/journal.ppat.1005308
call_split See protocol

[…] e reads were de-multiplexed and trimmed to remove bases with Phred scores < Q30. Reads were aligned to SC5314 reference genome using Bowtie2 (Version 2.0.7) [], and the alignment was visualized using Savant Genome Browser []. MuTect (Version 1.1.4) [] was used to identify unique mutations in filamentous C. albicans isolates. MuTect provides accurate variant detection in diploid genomes based on a […]

library_books

Variation detection based on next generation sequencing of type Chinese 1 strains of Toxoplasma gondii with different virulence from China

2015
BMC Genomics
PMCID: 4628340
PMID: 26518334
DOI: 10.1186/s12864-015-2106-z

[…] s than 20. The bam file produced from the mapping procedure was analyzed for structural variations (SVs) detection by BreakDancer [] with default parameters. SNPs, indels and SVs were displayed using Savant Genome Browser []. Copy number variations (CNVs) were detected with CALL in CNVnator []. Functional annotation of all the genetic variants was completed by ANNOVAR []. And the Circose plots wer […]


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Savant institution(s)
Department of Computer Science, University of Toronto, ON, Canada; Epigenetics Laboratory Cancer Research Program, Garvan Institute of Medical Research, Sydney, NSW, Australia; Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada; Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON, Canada; Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; Department of Biochemistry, University of Toronto, ON, Canada
Savant funding source(s)
Supported by CIHR Tools, Techniques and Innovation grant and MITACS Seed; the OGI SPARK, an NSERC Graduate Fellowship and Google Summer of Code.

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