@article{fdi:010076214,
  title = {{G}igwa v2-{E}xtended and improved genotype investigator},
  author = {{S}emp{\'e}r{\'e}, {G}. and {P}{\'e}tel, {A}. and {R}ouard, {M}. and {F}rouin, {J}. and {H}ueber, {Y}. and {D}e {B}ellis, {F}. and {L}armande, {P}ierre},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {T}he study of genetic variations is the basis of many research domains in biology. {F}rom genome structure to population dynamics, many applications involve the use of genetic variants. {T}he advent of next-generation sequencing technologies led to such a flood of data that the daily work of scientists is often more focused on data management than data analysis. {T}his mass of genotyping data poses several computational challenges in terms of storage, search, sharing, analysis, and visualization. {W}hile existing tools try to solve these challenges, few of them offer a comprehensive and scalable solution. {R}esults: {G}igwa v2 is an easy-to-use, species-agnostic web application for managing and exploring high-density genotyping data. {I}t can handle multiple databases and may be installed on a local computer or deployed as an online data portal. {I}t supports various standard import and export formats, provides advanced filtering options, and offers means to visualize density charts or push selected data into various stand-alone or online tools. {I}t implements 2 standard {REST}ful application programming interfaces, {GA}4{GH}, which is health-oriented, and {B}r{API}, which is breeding-oriented, thus offering wide possibilities of interaction with third-party applications. {T}he project home page provides a list of live instances allowing users to test the system on public data (or reasonably sized user-provided data). {C}onclusions: {T}his new version of {G}igwa provides a more intuitive and more powerful way to explore large amounts of genotyping data by offering a scalable solution to search for genotype patterns, functional annotations, or more complex filtering. {F}urthermore, its user-friendliness and interoperability make it widely accessible to the life science community.},
  keywords = {genomic variations ; {VCF} ; {H}ap{M}ap ; {PLINK} ; {N}o{SQL} ; {M}ongo{DB} ; {SNP} ; indel ; web ; interoperability ; {REST} ; {B}r{API} ; {GA}4{GH}},
  booktitle = {},
  journal = {{G}igascience},
  volume = {8},
  numero = {5},
  pages = {giz051 [9 p.]},
  ISSN = {2047-217{X}},
  year = {2019},
  DOI = {10.1093/gigascience/giz051},
  URL = {https://www.documentation.ird.fr/hor/fdi:010076214},
}