Supporting data and code for the African Rice Panreference produced by the frangiPANe software

Version 3.0

Tranchant, Christine; Chenal, Clothilde; Blaison, Mathieu; Albar, Laurence; Klein, Valentin; Mariac, Cédric; Wing, Rod; Vigouroux, Yves; Sabot, Francois, 2022, "Supporting data and code for the African Rice Panreference produced by the frangiPANe software", https://doi.org/10.23708/93OQMD, DataSuds, V3, UNF:6:J8wm0efC8Lf7KQQ/txrx4Q== [fileUNF]

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Description	We present here FrangiPANe (https://github.com/tranchant/frangiPANe), a pipeline developed to build panreference using short reads through a map-then-assemble strategy and a dataset corresponding to 515 Mb of new sequences (484,394 non redundant sequences) in addition to the CG14 genome (iOMAP consortium). Applying this approach to 248 African rice genomes, we identified an average of 8 Mb of new sequences and 5,290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1,306,676 contigs, were assembled. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2kb span. We annotated in addition 3,252 new genes absent from the reference. The authors acknowledge the IRD i-Trop HPC (South Green Platform) from IRD Montpellier for providing resources that contributed to this work. (2022-06-10)
Subject	Earth and Environmental Sciences
Keyword	pangenome, panreference, short reads, assembly, scability, map-then-assemble approach
Related Publication	FrangiPANe, a tool for creating a panreference using left behind reads
Notes	Data type: Analysis data; Process-produced data
License/Data Use Agreement	Custom Dataset Terms

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	1 to 4 of 4 Files	Original Format Archival Format (.tab)
	africanRice_nrctgs_readme.txt FrangiPANe/Plain Text - 1.8 KB Published Jan 27, 2023 7 Downloads MD5: 73de2fe097cfc2f4e5d5495f4dd1d765 Dataset citation, description and contents summary Documentation	Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	africanRice_nrctgs_V1.fasta FrangiPANe/Unknown - 504.0 MB Published Oct 26, 2022 9 Downloads MD5: 9d5d44f42a84c20758347c6b96246c01 Fasta file of the new sequences absent from the reference Data	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	africanRice_nrctgs_V1_placedOnGenome.tab FrangiPANe/Tabular Data - 4.6 MB Published Oct 26, 2022 6 Downloads 4 Variables, 152411 Observations UNF:6:J8wm0efC8Lf7KQQ/txrx4Q== CSV file with the position of the new sequences on the genome reference. It contains one line per sequence, each containing 4 columns : (1) the sequence id, (2) its length (bp), (3) the chromosome name, (4) its position on the chromosome. Data	Access File File Access Public Download Options Comma Separated Values (Original File Format) Tab-Delimited RData Download Metadata Variable Metadata Data File Citation EndNote XML RIS BibTeX
	frangiPANe-code-v1.zip FrangiPANe/ZIP Archive - 1.6 MB Published Jan 27, 2023 4 Downloads MD5: e1e2f64eaf0d3b9aa16dd6b745fde5ff frangiPANe source code, v1 (26-01-2023) - Jupyter Notebook application Code	Access File File Access Public Download Options ZIP Archive Download Metadata Data File Citation EndNote XML RIS BibTeX

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Persistent Identifier	doi:10.23708/93OQMD
Publication Date	2022-07-01
Title	Supporting data and code for the African Rice Panreference produced by the frangiPANe software
Author	Tranchant, Christine (UMR DIADE - IRD, University of Montpellier, Cirad - France) - ORCID: 0000-0001-6934-1215 Chenal, Clothilde (UMR MIVEGEC - CNRS, IRD - France) Blaison, Mathieu (UMR DIADE - IRD, University of Montpellier, Cirad - France) Albar, Laurence (UMR PHIM - CIRAD, INRAE, Institut Agro, IRD - France) Klein, Valentin (UMR DIADE - IRD, University of Montpellier, Cirad - France) Mariac, Cédric (UMR DIADE - IRD, University of Montpellier, Cirad - France) Wing, Rod (King Abdullah University of Science and Technology (KAUST) - Saudi Arabia) - ORCID: 0000-0001-6633-6226 Vigouroux, Yves (UMR DIADE - IRD, University of Montpellier, Cirad - France) - ORCID: 0000-0002-8361-6040 Sabot, Francois (UMR DIADE - IRD, University of Montpellier, Cirad - France) - ORCID: 0000-0002-8522-7583
Point of Contact	Use email button above to contact. Tranchant, Christine (UMR DIADE - IRD, University of Montpellier, Cirad - France)
Description	We present here FrangiPANe (https://github.com/tranchant/frangiPANe), a pipeline developed to build panreference using short reads through a map-then-assemble strategy and a dataset corresponding to 515 Mb of new sequences (484,394 non redundant sequences) in addition to the CG14 genome (iOMAP consortium). Applying this approach to 248 African rice genomes, we identified an average of 8 Mb of new sequences and 5,290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1,306,676 contigs, were assembled. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2kb span. We annotated in addition 3,252 new genes absent from the reference. The authors acknowledge the IRD i-Trop HPC (South Green Platform) from IRD Montpellier for providing resources that contributed to this work. (2022-06-10)
Subject	Earth and Environmental Sciences
Keyword	pangenome panreference short reads assembly scability map-then-assemble approach
Scientific Theme	Plant sciences (NumeriSud) https://uri.ird.fr/so/kos/tnu/076
Related Publication	FrangiPANe, a tool for creating a panreference using left behind reads
Notes	Data type: Analysis data; Process-produced data
Language	English
Funding Information	ANR: ANR-10-INBS-09 ANR: ANR-13-BSV7-0017
Depositor	Tranchant, Christine
Deposit Date	2022-06-10
Software	FrangiPANe, a tool for creating a panreference using left behind reads, Version: https://github.com/tranchant/frangiPANe docker, Version: https://docs.docker.com/get-docker/ Python3, Version: https://www.python.org/ Panel, Version: https://panel.holoviz.org/ abyss, Version: https://github.com/bcgsc/abyss/blob/master/README.md bwa, Version: https://github.com/lh3/bwa/blob/master/README.md ea-utils, Version: https://expressionanalysis.github.io/ea-utils/ samtools, Version: http://www.htslib.org/ assembly-stats, Version: https://github.com/sanger-pathogens/assembly-stats cd-hit, Version: https://github.com/weizhongli/cdhit/blob/master/README
Related Dataset	Cubry,P., Tranchant-Dubreuil,C., Thuillet,A.-C., Monat,C., Ndjiondjop,M.-N., Labadie,K., Cruaud,C., Engelen,S., Scarcelli,N., Rhoné,B., et al. (2018) The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes. Curr. Biol., 10.1016/j.cub.2018.05.066. Reference : more details Raw sequences : See on NCBI

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Geographic Bounding Box	-380.91796875000006 -317.63671875000006 27.059125784374068 -22.75592068148639

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