VOHG00000000.1 Taeniopygia guttata
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# of Contigs: 206 (206 are dead) # of Proteins: 0 # of Scaffolds/Chrs: 28 Total length: 1,042,306,463 bp BioProject: PRJNA489100 BioSample: SAMN09946140 Keywords: WGS Organism: Taeniopygia guttata – show lineagehide lineage Biosource: /collected_by = Matt Biegler, Duke University and Rockefeller University/country = USA/dev_stage = adult/isolate = Blue55/lat_lon = 36.0014 N 78.9382 W/mol_type = genomic/sex = female/tissue_type = Muscle, blood, brainWGS: VOHG01000001:VOHG01000206 Scaffolds: CM018261:CM018288 28 scaffolds, total length is 835,952,002 basesReference: G10K-VGP female zebra finch genome, maternal haplotype : Unpublished – show 19 authorshide authorsJarvis,E.D., Rhie,A., Fedrigo,O., Mountcastle,J., Biegler,M., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Formenti,G., Burt,D., Warren,W., Mello,C.V., Phillippy,A.Submission: Submitted (14-AUG-2019) Vertebrate Genomes Project, G10K, 1230 York Avenue, New York, NY 10065, USA – show 19 authorshide authorsJarvis,E.D., Rhie,A., Fedrigo,O., Mountcastle,J., Biegler,M., Howe,K., Wood,J., Lewin,H., Damas,J., Balakrishnan,C., Clayton,D., London,S., George,J., Haase,B., Formenti,G., Burt,D., Warren,W., Mello,C.V., Phillippy,A.[WARNING] On Nov 6, 2019 this project was updated. The new version is gi:1772843278.
The Taeniopygia guttata whole genome shotgun (WGS) project has the project accession VOHG00000000. This version of the project (01) has the accession number VOHG01000000, and consists of sequences VOHG01000001-VOHG01000206.
This assembly represents the maternal alternate haplotype of the diploid genome Taeniopygia guttata. The principal haplotype sequences of the VGP 1.5 trio assembly merged haplotype data are in WGS project VOHI00000000. The paternal alternate haploid sequences are in WGS project VOHH00000000. The bTaeGut2m assembly is based on the VGP 1.5 trio binning pipeline. Initial PacBio read binning into maternal and paternal haplotypes using parental Illumina short reads. Then each haplotype is assembled into contigs with Canu, followed by 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding with Bionano Solve, Hi-C based scaffolding with SALSA2, Arrow polishing and gap filling, and two rounds of FreeBayes polishing with Illumina short reads. This assembly was curated with chromosomes annotated using gEVAL before the FreeBayes polishing.
##Genome-Assembly-Data-START## Assembly Date : 24-MAY-2019 Assembly Method : Trio Binning v. 1; Canu v. 1.7; Scaff10x v. 2.1(git 4.28.2018); Bionano Solve 2 enzyme v. 3.2.1; Salsa2 v. 2.2; Arrow v. 5.1.0.26412; gEVAL manual curation v. 2019-05-24; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.2.0; VGP Trio binning assembly pipeline v. 1.5 Assembly Name : bTaeGut2m Diploid : Alternate pseudohaplotype Genome Representation : Full Expected Final Version : No Genome Coverage : 82.5x Sequencing Technology : PacBio Sequel; 10X genome; Bionano Genomics; Arima Genomics Hi-C; Illumina HiSeq ##Genome-Assembly-Data-END## - Contigs
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Minor Version Create Date 1 10/03/2019 2 11/06/2019 3 03/29/2020