Dataset for "Nanopore-based genome assembly and the evolutionary genomics of basmati rice"

<strong>Description of uploaded files:</strong> Basmati334.basmati.not_scaffolded.fa - Polished genome assembly for Basmati 334 but not scaffolded. Basmati334.basmati.not_scaffolded.sorted.gff - Gene annotation for the assembly Basmati334.basmati.not_scaffolded.fa Basmati334.basmati.ragoo_scaffold.fa - Polished genome assembly for Basmati 334 and scaffolding with RaGOO using the Nipponbare RAPDB1.0 as reference genome. Basmati334.basmati.ragoo_scaffold.sorted.gff - Gene annotation for the assembly Basmati334.basmati.ragoo_scaffold.fa Basmati334.basmati.ragoo_scaffold.repeatmasker.bed - Repetitive DNA coordinates for the assembly Basmati334.basmati.ragoo_scaffold.fa CONSEL.tar.gz - Files used for CONSEL analysis - Folder CONSEL/PHYLOGENY_TEST/ contains the input files for CONSEL - Folder CONSEL/CONSEL_RESULT/ contains the CONSEL test results DADI_ANALYSIS.tar.gz - Input file for dadi analysis and scripts used for dadi modeling DomSufid.sadri.not_scaffolded.fa - Polished genome assembly for Dom Sufid but not scaffolded. DomSufid.sadri.not_scaffolded.sorted.gff - Gene annotation for the assembly DomSufid.sadri.not_scaffolded.fa DomSufid.sadri.ragoo_scaffold.fa - Polished genome assembly for Dom Sufid and scaffolding with RaGOO using the Nipponbare RAPDB1.0 as reference genome. DomSufid.sadri.ragoo_scaffold.sorted.gff - Gene annotation for the assembly DomSufid.sadri.ragoo_scaffold.fa DomSufid.sadri.ragoo_scaffold.repeatmasker.bed - Repetitive DNA coordinates for the assembly DomSufid.sadri.ragoo_scaffold.fa Four_rice_population.vcf.gz - Filtered SNP VCF file used in the basmati population relationship with japonica and aus. MULTIZ_ALIGNMENT.tar.gz - Reference genome alignment using Nipponbare RAPDB1.0 as reference and aligning various Oryza de novo genome assemblies Multi_Oryza_gene_FASTAs.tar.gz - Using the alignments from MULTIZ_ALIGNMENT/ pulled out coding DNA sequences of each Nipponbare RAPDB1.0 gene Obarthii_outgroup_AlignedToBasmatiScaffolded_genome.fa - O. barthii reference genome sequence was aligned to scaffolded Basmati 334 reference genome. For every Basmati 334 genome coordinate was converted into a O. barthii sequence resulting in a basmati-ized O. barthii genome sequence. Not alignable regions were indicated as 'N'. Only_basmati_rice_population.vcf.gz - Filtered SNP VCF file used in the basmati population analysis. Oryza_LTR_DivergenceTime.txt - LTR retrotransposon annotated in various Oryza reference genomes and their estimated insertion time (based on the divergence between the LTRs). TWISST.tar.gz - TWISST input and results file. - Four_rice_population.geno.gz, genotype file generated from the genomic_general from S. Martin and used as input for TWISST analysis. - *.trees.gz phylogenetic trees generated from sliding windows - *.data.tsv sliding window coordinates - *.weights.csv.gz topology weights