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By the same authors

GAMUT: A Genomics Big Data Management Tool

Research output: Contribution to journalArticlepeer-review

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GAMUT: A Genomics Big Data Management Tool. / Ramakrishnan, E P ; Gupta, Saurabh ; Gadhari, Renu ; Bharti, Neeraj ; Malviya, Sandeep; Manjari Kasibhatla, Sunitha ; Kim, Jan T; Joshi, Rajendra .

In: Journal do Biosciences, Vol. 46, 89, 08.09.2021.

Research output: Contribution to journalArticlepeer-review

Harvard

Ramakrishnan, EP, Gupta, S, Gadhari, R, Bharti, N, Malviya, S, Manjari Kasibhatla, S, Kim, JT & Joshi, R 2021, 'GAMUT: A Genomics Big Data Management Tool', Journal do Biosciences, vol. 46, 89. https://doi.org/10.1007/s12038-021-00213-y

APA

Ramakrishnan, E. P., Gupta, S., Gadhari, R., Bharti, N., Malviya, S., Manjari Kasibhatla, S., Kim, J. T., & Joshi, R. (2021). GAMUT: A Genomics Big Data Management Tool. Journal do Biosciences, 46, [89]. https://doi.org/10.1007/s12038-021-00213-y

Vancouver

Ramakrishnan EP, Gupta S, Gadhari R, Bharti N, Malviya S, Manjari Kasibhatla S et al. GAMUT: A Genomics Big Data Management Tool. Journal do Biosciences. 2021 Sep 8;46. 89. https://doi.org/10.1007/s12038-021-00213-y

Author

Ramakrishnan, E P ; Gupta, Saurabh ; Gadhari, Renu ; Bharti, Neeraj ; Malviya, Sandeep ; Manjari Kasibhatla, Sunitha ; Kim, Jan T ; Joshi, Rajendra . / GAMUT: A Genomics Big Data Management Tool. In: Journal do Biosciences. 2021 ; Vol. 46.

Bibtex

@article{ca9be805571742ee8b468154f60f5219,
title = "GAMUT: A Genomics Big Data Management Tool",
abstract = "Efficient analysis of Single Nucleotide Polymorphisms (SNPs) across genomic samples enable in deciphering the relationship between genotype and phenotype. The core principle behind SNP comparison is to arrive at a probable list of variants that can differentiate two sets of data (populations). Such SNPs have direct applications in array design, genotype imputation and in cataloging of variants in regions of interest. We have developed GAMUT (Genomics bigdAta Management Tool), a big data-based solution for efficient run-time comparison of SNPs across large datasets based on partition of samples belonging to different populations taking into account user-defined splits. The tool is based on client-server architecture with MongoDB at the back-end and JSF with PrimeFaces as the front-end. It is readily deployable on wild-fly server as well as a docker container. Spark-based parallel data uploader enables optimal loading times. GAMUT enables dynamic querying of the large datasets consisting of multiple samples using text-based, chromosome position-based as well as gene-name based options. Various charting options like bar and pie charts along with tabular formats are available to ease the analysis of the queried data. The resultant data pertaining to comparison of genome-wide SNPs can also be downloaded in different formats like text, html, json for further stand-alone analysis. GAMUT is available for download at: https://github.com/bioinformatics-cdac/gamut",
keywords = "Big data, NGS, SNP, database, genomics, variant comparison, vcf",
author = "Ramakrishnan, {E P} and Saurabh Gupta and Renu Gadhari and Neeraj Bharti and Sandeep Malviya and {Manjari Kasibhatla}, Sunitha and Kim, {Jan T} and Rajendra Joshi",
note = "{\textcopyright} Indian Academy of Sciences. ",
year = "2021",
month = sep,
day = "8",
doi = "10.1007/s12038-021-00213-y",
language = "English",
volume = "46",
journal = "Journal do Biosciences",
issn = "0973-7138",

}

RIS

TY - JOUR

T1 - GAMUT: A Genomics Big Data Management Tool

AU - Ramakrishnan, E P

AU - Gupta, Saurabh

AU - Gadhari, Renu

AU - Bharti, Neeraj

AU - Malviya, Sandeep

AU - Manjari Kasibhatla, Sunitha

AU - Kim, Jan T

AU - Joshi, Rajendra

N1 - © Indian Academy of Sciences.

PY - 2021/9/8

Y1 - 2021/9/8

N2 - Efficient analysis of Single Nucleotide Polymorphisms (SNPs) across genomic samples enable in deciphering the relationship between genotype and phenotype. The core principle behind SNP comparison is to arrive at a probable list of variants that can differentiate two sets of data (populations). Such SNPs have direct applications in array design, genotype imputation and in cataloging of variants in regions of interest. We have developed GAMUT (Genomics bigdAta Management Tool), a big data-based solution for efficient run-time comparison of SNPs across large datasets based on partition of samples belonging to different populations taking into account user-defined splits. The tool is based on client-server architecture with MongoDB at the back-end and JSF with PrimeFaces as the front-end. It is readily deployable on wild-fly server as well as a docker container. Spark-based parallel data uploader enables optimal loading times. GAMUT enables dynamic querying of the large datasets consisting of multiple samples using text-based, chromosome position-based as well as gene-name based options. Various charting options like bar and pie charts along with tabular formats are available to ease the analysis of the queried data. The resultant data pertaining to comparison of genome-wide SNPs can also be downloaded in different formats like text, html, json for further stand-alone analysis. GAMUT is available for download at: https://github.com/bioinformatics-cdac/gamut

AB - Efficient analysis of Single Nucleotide Polymorphisms (SNPs) across genomic samples enable in deciphering the relationship between genotype and phenotype. The core principle behind SNP comparison is to arrive at a probable list of variants that can differentiate two sets of data (populations). Such SNPs have direct applications in array design, genotype imputation and in cataloging of variants in regions of interest. We have developed GAMUT (Genomics bigdAta Management Tool), a big data-based solution for efficient run-time comparison of SNPs across large datasets based on partition of samples belonging to different populations taking into account user-defined splits. The tool is based on client-server architecture with MongoDB at the back-end and JSF with PrimeFaces as the front-end. It is readily deployable on wild-fly server as well as a docker container. Spark-based parallel data uploader enables optimal loading times. GAMUT enables dynamic querying of the large datasets consisting of multiple samples using text-based, chromosome position-based as well as gene-name based options. Various charting options like bar and pie charts along with tabular formats are available to ease the analysis of the queried data. The resultant data pertaining to comparison of genome-wide SNPs can also be downloaded in different formats like text, html, json for further stand-alone analysis. GAMUT is available for download at: https://github.com/bioinformatics-cdac/gamut

KW - Big data

KW - NGS

KW - SNP

KW - database

KW - genomics

KW - variant comparison

KW - vcf

UR - http://www.scopus.com/inward/record.url?scp=85114461110&partnerID=8YFLogxK

U2 - 10.1007/s12038-021-00213-y

DO - 10.1007/s12038-021-00213-y

M3 - Article

VL - 46

JO - Journal do Biosciences

JF - Journal do Biosciences

SN - 0973-7138

M1 - 89

ER -