{"id":"https://openalex.org/W2191913882","doi":"https://doi.org/10.1186/s12859-015-0795-6","title":"TOGGLE: toolbox for generic NGS analyses","display_name":"TOGGLE: toolbox for generic NGS analyses","publication_year":2015,"publication_date":"2015-11-09","ids":{"openalex":"https://openalex.org/W2191913882","doi":"https://doi.org/10.1186/s12859-015-0795-6","mag":"2191913882","pmid":"https://pubmed.ncbi.nlm.nih.gov/26552596"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0795-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0795-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0795-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0795-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012594830","display_name":"C\u00e9cile Monat","orcid":"https://orcid.org/0000-0002-0574-3976"},"institutions":[{"id":"https://openalex.org/I251321805","display_name":"Agropolis International","ror":"https://ror.org/00txxwv34","country_code":"FR","type":"other","lineage":["https://openalex.org/I251321805"]},{"id":"https://openalex.org/I4210117822","display_name":"Diversit\u00e9, adaptation et d\u00e9veloppement des plantes","ror":"https://ror.org/02banhz78","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I19894307","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210117822","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"C\u00e9cile Monat","raw_affiliation_strings":["UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. cecile.monat@ird.fr","UMR DIADE - Diversit\u00e9, adaptation, d\u00e9veloppement des plantes (Centre IRD de Montpellier 911 av Agropolis BP 604501 34394 Montpellier cedex 5 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. cecile.monat@ird.fr","institution_ids":["https://openalex.org/I4210166444","https://openalex.org/I251321805"]},{"raw_affiliation_string":"UMR DIADE - Diversit\u00e9, adaptation, d\u00e9veloppement des plantes (Centre IRD de Montpellier 911 av Agropolis BP 604501 34394 Montpellier cedex 5 - France)","institution_ids":["https://openalex.org/I4210166444","https://openalex.org/I251321805","https://openalex.org/I4210117822"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081141425","display_name":"Christine Tranchant\u2010Dubreuil","orcid":"https://orcid.org/0000-0001-6934-1215"},"institutions":[{"id":"https://openalex.org/I251321805","display_name":"Agropolis International","ror":"https://ror.org/00txxwv34","country_code":"FR","type":"other","lineage":["https://openalex.org/I251321805"]},{"id":"https://openalex.org/I4210117822","display_name":"Diversit\u00e9, adaptation et d\u00e9veloppement des plantes","ror":"https://ror.org/02banhz78","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I19894307","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210117822","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Christine Tranchant-Dubreuil","raw_affiliation_strings":["UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. christine.tranchant@ird.fr","UMR DIADE - Diversit\u00e9, adaptation, d\u00e9veloppement des plantes (Centre IRD de Montpellier 911 av Agropolis BP 604501 34394 Montpellier cedex 5 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. christine.tranchant@ird.fr","institution_ids":["https://openalex.org/I4210166444","https://openalex.org/I251321805"]},{"raw_affiliation_string":"UMR DIADE - Diversit\u00e9, adaptation, d\u00e9veloppement des plantes (Centre IRD de Montpellier 911 av Agropolis BP 604501 34394 Montpellier cedex 5 - France)","institution_ids":["https://openalex.org/I4210166444","https://openalex.org/I251321805","https://openalex.org/I4210117822"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010916656","display_name":"Ayit\u00e9 Kougbeadjo","orcid":"https://orcid.org/0000-0002-7230-6362"},"institutions":[{"id":"https://openalex.org/I131077856","display_name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique pour le D\u00e9veloppement","ror":"https://ror.org/05kpkpg04","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856"]},{"id":"https://openalex.org/I251321805","display_name":"Agropolis International","ror":"https://ror.org/00txxwv34","country_code":"FR","type":"other","lineage":["https://openalex.org/I251321805"]},{"id":"https://openalex.org/I4210120904","display_name":"Am\u00e9lioration G\u00e9n\u00e9tique et Adaptation des Plantes m\u00e9diterran\u00e9ennes et tropicales","ror":"https://ror.org/02w4exq36","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856","https://openalex.org/I19894307","https://openalex.org/I24906876","https://openalex.org/I4210088668","https://openalex.org/I4210117091","https://openalex.org/I4210120904","https://openalex.org/I4399657933"]},{"id":"https://openalex.org/I4210136436","display_name":"Institut Agro Montpelier","ror":null,"country_code":"FR","type":null,"lineage":["https://openalex.org/I4210136436"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ayit\u00e9 Kougbeadjo","raw_affiliation_strings":["UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. ayite.kougbeadjo@cirad.fr","UMR AGAP - Am\u00e9lioration g\u00e9n\u00e9tique et adaptation des plantes m\u00e9diterran\u00e9ennes et tropicales (TA A-108 / 03 - Avenue Agropolis - 34398 Montpellier Cedex 5 France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. ayite.kougbeadjo@cirad.fr","institution_ids":["https://openalex.org/I131077856","https://openalex.org/I4210136436","https://openalex.org/I251321805","https://openalex.org/I4210120904"]},{"raw_affiliation_string":"UMR AGAP - Am\u00e9lioration g\u00e9n\u00e9tique et adaptation des plantes m\u00e9diterran\u00e9ennes et tropicales (TA A-108 / 03 - Avenue Agropolis - 34398 Montpellier Cedex 5 France - France)","institution_ids":["https://openalex.org/I4210120904","https://openalex.org/I251321805"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026367112","display_name":"C\u00e9dric Farcy","orcid":null},"institutions":[{"id":"https://openalex.org/I131077856","display_name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique pour le D\u00e9veloppement","ror":"https://ror.org/05kpkpg04","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856"]},{"id":"https://openalex.org/I251321805","display_name":"Agropolis International","ror":"https://ror.org/00txxwv34","country_code":"FR","type":"other","lineage":["https://openalex.org/I251321805"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210120904","display_name":"Am\u00e9lioration G\u00e9n\u00e9tique et Adaptation des Plantes m\u00e9diterran\u00e9ennes et tropicales","ror":"https://ror.org/02w4exq36","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856","https://openalex.org/I19894307","https://openalex.org/I24906876","https://openalex.org/I4210088668","https://openalex.org/I4210117091","https://openalex.org/I4210120904","https://openalex.org/I4399657933"]},{"id":"https://openalex.org/I4210136436","display_name":"Institut Agro Montpelier","ror":null,"country_code":"FR","type":null,"lineage":["https://openalex.org/I4210136436"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"C\u00e9dric Farcy","raw_affiliation_strings":["UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. cedric.farcy@cirad.fr","INRA - Institut National de la Recherche Agronomique (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. cedric.farcy@cirad.fr","institution_ids":["https://openalex.org/I131077856","https://openalex.org/I4210136436","https://openalex.org/I251321805","https://openalex.org/I4210120904"]},{"raw_affiliation_string":"INRA - Institut National de la Recherche Agronomique (France)","institution_ids":["https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058493715","display_name":"Enrique Ortega\u2010Abboud","orcid":"https://orcid.org/0000-0001-6974-839X"},"institutions":[{"id":"https://openalex.org/I131077856","display_name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique pour le D\u00e9veloppement","ror":"https://ror.org/05kpkpg04","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856"]},{"id":"https://openalex.org/I251321805","display_name":"Agropolis International","ror":"https://ror.org/00txxwv34","country_code":"FR","type":"other","lineage":["https://openalex.org/I251321805"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210136436","display_name":"Institut Agro Montpelier","ror":null,"country_code":"FR","type":null,"lineage":["https://openalex.org/I4210136436"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Enrique Ortega-Abboud","raw_affiliation_strings":["UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. enrique.ortega-abboud@cirad.fr","INRA - Institut National de la Recherche Agronomique (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. enrique.ortega-abboud@cirad.fr","institution_ids":["https://openalex.org/I131077856","https://openalex.org/I4210136436","https://openalex.org/I251321805"]},{"raw_affiliation_string":"INRA - Institut National de la Recherche Agronomique (France)","institution_ids":["https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061857985","display_name":"Souhila Amanzougarene","orcid":null},"institutions":[{"id":"https://openalex.org/I251321805","display_name":"Agropolis International","ror":"https://ror.org/00txxwv34","country_code":"FR","type":"other","lineage":["https://openalex.org/I251321805"]},{"id":"https://openalex.org/I4210117822","display_name":"Diversit\u00e9, adaptation et d\u00e9veloppement des plantes","ror":"https://ror.org/02banhz78","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I19894307","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210117822","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Souhila Amanzougarene","raw_affiliation_strings":["UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. souhila.amanzougarene@ird.fr","UMR DIADE - Diversit\u00e9, adaptation, d\u00e9veloppement des plantes (Centre IRD de Montpellier 911 av Agropolis BP 604501 34394 Montpellier cedex 5 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. souhila.amanzougarene@ird.fr","institution_ids":["https://openalex.org/I4210166444","https://openalex.org/I251321805"]},{"raw_affiliation_string":"UMR DIADE - Diversit\u00e9, adaptation, d\u00e9veloppement des plantes (Centre IRD de Montpellier 911 av Agropolis BP 604501 34394 Montpellier cedex 5 - France)","institution_ids":["https://openalex.org/I4210166444","https://openalex.org/I251321805","https://openalex.org/I4210117822"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071399944","display_name":"S\u00e9bastien Ravel","orcid":"https://orcid.org/0000-0001-6663-782X"},"institutions":[{"id":"https://openalex.org/I131077856","display_name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique pour le D\u00e9veloppement","ror":"https://ror.org/05kpkpg04","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856"]},{"id":"https://openalex.org/I4210087514","display_name":"Biologie et G\u00e9n\u00e9tique des Interactions Plante-Parasite","ror":"https://ror.org/0026vdt21","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856","https://openalex.org/I24906876","https://openalex.org/I4210087514","https://openalex.org/I4210088668","https://openalex.org/I4210117091","https://openalex.org/I4399657933"]},{"id":"https://openalex.org/I4210126969","display_name":"Forests and Societies","ror":"https://ror.org/02pzyz439","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856","https://openalex.org/I19894307","https://openalex.org/I4210126969"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"S\u00e9bastien Ravel","raw_affiliation_strings":["UMR-BGPI CIRAD TA A-54/K, Campus International de Baillarguet, Montpellier Cedex 5, F-34398, France. sebastien.ravel@cirad.fr","UMR BGPI - Biologie et G\u00e9n\u00e9tique des Interactions Plante-Parasite (CIRAD\r\nUMR-BGPI TA A-54/K - Campus International de Baillarguet - 34398 Montpellier Cedex 5 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR-BGPI CIRAD TA A-54/K, Campus International de Baillarguet, Montpellier Cedex 5, F-34398, France. sebastien.ravel@cirad.fr","institution_ids":["https://openalex.org/I131077856","https://openalex.org/I4210126969","https://openalex.org/I4210087514"]},{"raw_affiliation_string":"UMR BGPI - Biologie et G\u00e9n\u00e9tique des Interactions Plante-Parasite (CIRAD\r\nUMR-BGPI TA A-54/K - Campus International de Baillarguet - 34398 Montpellier Cedex 5 - France)","institution_ids":["https://openalex.org/I4210087514","https://openalex.org/I131077856"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055663494","display_name":"Mawuss\u00e9 Agbessi","orcid":"https://orcid.org/0000-0002-8956-5299"},"institutions":[{"id":"https://openalex.org/I251321805","display_name":"Agropolis International","ror":"https://ror.org/00txxwv34","country_code":"FR","type":"other","lineage":["https://openalex.org/I251321805"]},{"id":"https://openalex.org/I4210117822","display_name":"Diversit\u00e9, adaptation et d\u00e9veloppement des plantes","ror":"https://ror.org/02banhz78","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I19894307","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210117822","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Mawuss\u00e9 Agbessi","raw_affiliation_strings":["UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. mawusse.agbessi@ird.fr","UMR DIADE - Diversit\u00e9, adaptation, d\u00e9veloppement des plantes (Centre IRD de Montpellier 911 av Agropolis BP 604501 34394 Montpellier cedex 5 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. mawusse.agbessi@ird.fr","institution_ids":["https://openalex.org/I4210166444","https://openalex.org/I251321805"]},{"raw_affiliation_string":"UMR DIADE - Diversit\u00e9, adaptation, d\u00e9veloppement des plantes (Centre IRD de Montpellier 911 av Agropolis BP 604501 34394 Montpellier cedex 5 - France)","institution_ids":["https://openalex.org/I4210166444","https://openalex.org/I251321805","https://openalex.org/I4210117822"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000270750","display_name":"Julie Orjuela","orcid":"https://orcid.org/0000-0001-8387-2266"},"institutions":[{"id":"https://openalex.org/I3908793","display_name":"Alpha MOS (France)","ror":"https://ror.org/059spgx09","country_code":"FR","type":"company","lineage":["https://openalex.org/I3908793"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Julie Orjuela-Bouniol","raw_affiliation_strings":["ADNid, Cap Alpha, Avenue de l'Europe, Clapiers, F-34830, France. julie.orjuela@adnid.fr","ADNid (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ADNid, Cap Alpha, Avenue de l'Europe, Clapiers, F-34830, France. julie.orjuela@adnid.fr","institution_ids":["https://openalex.org/I3908793"]},{"raw_affiliation_string":"ADNid (France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003962508","display_name":"Marilyne Summo","orcid":"https://orcid.org/0000-0002-9308-974X"},"institutions":[{"id":"https://openalex.org/I131077856","display_name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique pour le D\u00e9veloppement","ror":"https://ror.org/05kpkpg04","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856"]},{"id":"https://openalex.org/I251321805","display_name":"Agropolis International","ror":"https://ror.org/00txxwv34","country_code":"FR","type":"other","lineage":["https://openalex.org/I251321805"]},{"id":"https://openalex.org/I4210120904","display_name":"Am\u00e9lioration G\u00e9n\u00e9tique et Adaptation des Plantes m\u00e9diterran\u00e9ennes et tropicales","ror":"https://ror.org/02w4exq36","country_code":"FR","type":"facility","lineage":["https://openalex.org/I131077856","https://openalex.org/I19894307","https://openalex.org/I24906876","https://openalex.org/I4210088668","https://openalex.org/I4210117091","https://openalex.org/I4210120904","https://openalex.org/I4399657933"]},{"id":"https://openalex.org/I4210136436","display_name":"Institut Agro Montpelier","ror":null,"country_code":"FR","type":null,"lineage":["https://openalex.org/I4210136436"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Maryline Summo","raw_affiliation_strings":["UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. maryline.summo@cirad.fr","UMR AGAP - Am\u00e9lioration g\u00e9n\u00e9tique et adaptation des plantes m\u00e9diterran\u00e9ennes et tropicales (TA A-108 / 03 - Avenue Agropolis - 34398 Montpellier Cedex 5 France - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR AGAP CIRAD/INRA/SupAgro, TA A-108/03 - Avenue Agropolis, Montpellier Cedex 5, F-34398, France. maryline.summo@cirad.fr","institution_ids":["https://openalex.org/I131077856","https://openalex.org/I4210136436","https://openalex.org/I251321805","https://openalex.org/I4210120904"]},{"raw_affiliation_string":"UMR AGAP - Am\u00e9lioration g\u00e9n\u00e9tique et adaptation des plantes m\u00e9diterran\u00e9ennes et tropicales (TA A-108 / 03 - Avenue Agropolis - 34398 Montpellier Cedex 5 France - France)","institution_ids":["https://openalex.org/I4210120904","https://openalex.org/I251321805"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061279430","display_name":"Fran\u00e7ois Sabot","orcid":"https://orcid.org/0000-0002-8522-7583"},"institutions":[{"id":"https://openalex.org/I251321805","display_name":"Agropolis International","ror":"https://ror.org/00txxwv34","country_code":"FR","type":"other","lineage":["https://openalex.org/I251321805"]},{"id":"https://openalex.org/I4210117822","display_name":"Diversit\u00e9, adaptation et d\u00e9veloppement des plantes","ror":"https://ror.org/02banhz78","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I19894307","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210117822","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Fran\u00e7ois Sabot","raw_affiliation_strings":["UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. francois.sabot@ird.fr","UMR DIADE - Diversit\u00e9, adaptation, d\u00e9veloppement des plantes (Centre IRD de Montpellier 911 av Agropolis BP 604501 34394 Montpellier cedex 5 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR DIADE IRD/UM, 911 Avenue Agropolis, Montpellier Cedex 5, F-34934, France. francois.sabot@ird.fr","institution_ids":["https://openalex.org/I4210166444","https://openalex.org/I251321805"]},{"raw_affiliation_string":"UMR DIADE - Diversit\u00e9, adaptation, d\u00e9veloppement des plantes (Centre IRD de Montpellier 911 av Agropolis BP 604501 34394 Montpellier cedex 5 - France)","institution_ids":["https://openalex.org/I4210166444","https://openalex.org/I251321805","https://openalex.org/I4210117822"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5061279430","https://openalex.org/A5081141425"],"corresponding_institution_ids":["https://openalex.org/I251321805","https://openalex.org/I4210117822","https://openalex.org/I4210166444"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.6257,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.8378936,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"374","last_page":"374"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.2897000014781952,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.2897000014781952,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.2825999855995178,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.09059999883174896,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8409675359725952},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.8359189629554749},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.7155520915985107},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7034016251564026},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.6035779714584351},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.5326730012893677},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5088420510292053},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.48644208908081055},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4790245592594147},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4274931252002716},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.42381733655929565},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.311576783657074},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.25573208928108215}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8409675359725952},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8359189629554749},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.7155520915985107},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7034016251564026},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.6035779714584351},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.5326730012893677},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5088420510292053},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.48644208908081055},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4790245592594147},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4274931252002716},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.42381733655929565},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.311576783657074},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.25573208928108215},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-015-0795-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0795-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0795-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26552596","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26552596","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:HAL:hal-02638152v1","is_oa":true,"landing_page_url":"https://hal.inrae.fr/hal-02638152","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://bmcbioinformatics.biomedcentral.com/","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:agritrop.cirad.fr:579008","is_oa":true,"landing_page_url":"http://agritrop.cirad.fr/579008/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402311","display_name":"Agritrop (Cirad)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I131077856","host_organization_name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique pour le D\u00e9veloppement","host_organization_lineage":["https://openalex.org/I131077856"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:3613784","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4640241","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0795-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0795-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0795-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1448097330","display_name":null,"funder_award_id":"1403-026","funder_id":"https://openalex.org/F4320309924","funder_display_name":"Agropolis Fondation"},{"id":"https://openalex.org/G4080994714","display_name":null,"funder_award_id":"1202-040","funder_id":"https://openalex.org/F4320309924","funder_display_name":"Agropolis Fondation"},{"id":"https://openalex.org/G4339915036","display_name":"Agricultural Sciences for sustainable Development","funder_award_id":"ANR-10-LABX-0001","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G5087811111","display_name":null,"funder_award_id":"ANR-10-LABX-0001-01","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G6857972019","display_name":null,"funder_award_id":"ID 1403-026","funder_id":"https://openalex.org/F4320309924","funder_display_name":"Agropolis Fondation"},{"id":"https://openalex.org/G7240651115","display_name":null,"funder_award_id":"ANR-10","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7376787254","display_name":null,"funder_award_id":"ANR-10-LABX","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7672827351","display_name":null,"funder_award_id":"ANR-10-LABX-0001-01","funder_id":"https://openalex.org/F4320309924","funder_display_name":"Agropolis Fondation"},{"id":"https://openalex.org/G946110321","display_name":"Documenting African Crop Domestication","funder_award_id":"ANR-13-BSV7-0017","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320309924","display_name":"Agropolis Fondation","ror":"https://ror.org/05kpkpg04"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320324228","display_name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique pour le D\u00e9veloppement","ror":"https://ror.org/05kpkpg04"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2191913882.pdf","grobid_xml":"https://content.openalex.org/works/W2191913882.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W2000894445","https://openalex.org/W2036897871","https://openalex.org/W2038733937","https://openalex.org/W2065817684","https://openalex.org/W2069577154","https://openalex.org/W2103441770","https://openalex.org/W2107549082","https://openalex.org/W2108234281","https://openalex.org/W2117716708","https://openalex.org/W2119180969","https://openalex.org/W2131187246","https://openalex.org/W2134526812","https://openalex.org/W2136482257","https://openalex.org/W2168103533","https://openalex.org/W2168440186"],"related_works":["https://openalex.org/W2068663075","https://openalex.org/W4205140848","https://openalex.org/W2978678743","https://openalex.org/W2797837731","https://openalex.org/W2150344375","https://openalex.org/W829257147","https://openalex.org/W2265275674","https://openalex.org/W2058034687","https://openalex.org/W2390579056","https://openalex.org/W2351397565"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,19,204],"explosion":[2],"of":[3,21,31,75,85,101,134,148,170,184,196],"NGS":[4,86],"(Next":[5],"Generation":[6],"Sequencing)":[7],"sequence":[8],"data":[9,36,40,178,209],"requires":[10],"a":[11,42,56,73,110,137,158,181],"huge":[12],"effort":[13],"in":[14,45,108,136,154],"Bioinformatics":[15],"methods":[16],"and":[17,24,58,88,177,198,207],"analyses.":[18,185],"creation":[20,169],"dedicated,":[22],"robust":[23,171],"reliable":[25,174],"pipelines":[26,80,107,172],"able":[27,77],"to":[28,37,78,96,124,152,161,190],"handle":[29],"dozens":[30],"samples":[32],"from":[33],"raw":[34],"FASTQ":[35],"relevant":[38],"biological":[39,194],"is":[41,72],"time-consuming":[43],"task":[44],"all":[46],"projects":[47],"relying":[48],"on":[49,192],"NGS.":[50],"To":[51],"address":[52],"this,":[53],"we":[54],"created":[55],"generic":[57],"modular":[59],"toolbox":[60],"for":[61,68,119,142,145,180],"developing":[62],"such":[63],"pipelines.":[64],"RESULTS:":[65],"TOGGLE":[66,91,135,165],"(TOolbox":[67],"Generic":[69],"nGs":[70],"anaLysEs)":[71],"suite":[74],"tools":[76],"design":[79],"that":[81],"manage":[82],"large":[83,146,182],"sets":[84,147],"softwares":[87,104],"utilities.":[89],"Moreover,":[90,186],"offers":[92],"an":[93],"easy":[94],"way":[95],"manipulate":[97],"the":[98,102,106,126,168,193,200],"various":[99],"options":[100],"different":[103,155],"through":[105],"using":[109],"single":[111,159],"basic":[112],"configuration":[113],"file,":[114],"which":[115],"can":[116],"be":[117],"changed":[118],"each":[120],"assay":[121],"without":[122],"having":[123],"change":[125,199],"code":[127,206],"itself.":[128],"We":[129],"also":[130],"describe":[131],"one":[132],"implementation":[133],"complete":[138],"analysis":[139],"pipeline":[140],"designed":[141],"SNP":[143],"discovery":[144],"genomic":[149],"data,":[150],"ready":[151],"use":[153],"environments":[156],"(from":[157],"machine":[160],"HPC":[162],"clusters).":[163],"CONCLUSION:":[164],"speeds":[166],"up":[167],"with":[173],"log":[175],"tracking":[176],"flow,":[179],"range":[183],"it":[187],"enables":[188],"Biologists":[189],"concentrate":[191],"relevance":[195],"results,":[197],"experimental":[201],"conditions":[202],"easily.":[203],"whole":[205],"test":[208],"are":[210],"available":[211],"at":[212],"https://github.com/SouthGreenPlatform/TOGGLE":[213],".":[214]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2}],"updated_date":"2026-07-08T08:33:18.762332","created_date":"2025-10-10T00:00:00"}
