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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 in pipelines

 (5)
2016
PMCID: 5078920
PMID: 27776542
DOI: 10.1186/s13059-016-1079-9

[…] 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 []., additional file 1: , we thank gideon rechavi, eli eisenberg, and members of the levanon lab for their helpful discussions. we also thank hagit porath and ilana buchumenski […]

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

[…] 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 […]

2015
PMCID: 4654494
PMID: 26588216
DOI: 10.1371/journal.ppat.1005308

[…] 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 […]

2014
PMCID: 3990763
PMID: 24748858
DOI: 10.5808/GI.2014.12.1.21

[…] for analyzing the genomic topography of alternations or for inspecting particular genomic loci []. typical techniques in this approach are genomics viewer [], ucsc cancer denomics browser [], and savant genome browser [].- networks (or graphs) can be used to show changes in state for 1) interpreting and exploring large biological networks and 2) assembly and curation of pathways (such […]

2014
PMCID: 3990763
PMID: 24748858
DOI: 10.5808/GI.2014.12.1.21

[…] for analyzing the genomic topography of alternations or for inspecting particular genomic loci []. typical techniques in this approach are genomics viewer [], ucsc cancer denomics browser [], and savant genome browser []., - networks (or graphs) can be used to show changes in state for 1) interpreting and exploring large biological networks and 2) assembly and curation of pathways (such […]


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Savant in publications

 (16)
PMCID: 5876298
PMID: 29628913
DOI: 10.3389/fmicb.2018.00520

[…] 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 […]

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

[…] 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 […]

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

[…] 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, […]

PMCID: 4945830
PMID: 26463000
DOI: 10.1093/bib/bbv080

[…] overviews of visualization tools are available [], and this section only briefly surveys a few of the most popular alternatives., genome browsers such as the ucsc cancer genomics browser [] and the savant genome browser [] allow data visualization by genomic location, with addition of annotations and data types as additional tracks. the integrative genomics viewer [] additionally enables […]

PMCID: 4585241
PMID: 26441923
DOI: 10.3389/fmicb.2015.00996

[…] recalibrate base quality scores, and locally realign regions around indels. all polymorphisms in both bo5.10 (82,212 bp) and the polygalacturonase genes (5492 bp × 13) were visually checked using savant (fiume et al., )., initially, the first round vcf file produced by gatk unifiedgenotyper was filtered by removing anything with < 6x coverage and quality threshold of 30, which gave zero […]


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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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