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

<p><strong>Description of uploaded files:</strong></p> <p>Basmati334.basmati.not_scaffolded.fa</p> <p>- Polished genome assembly for Basmati 334 but not scaffolded.</p> <p>&nbsp;</p> <p>Basmati334.basmati.not_scaffolded.sorted.gff</p> <p>- Gene annotation for the assembly&nbsp;Basmati334.basmati.not_scaffolded.fa</p> <p>&nbsp;</p> <p>Basmati334.basmati.ragoo_scaffold.fa</p> <p>- Polished genome assembly for Basmati 334 and scaffolding with RaGOO using the Nipponbare RAPDB1.0 as reference genome.</p> <p>&nbsp;</p> <p>Basmati334.basmati.ragoo_scaffold.sorted.gff</p> <p>-&nbsp;Gene annotation for the assembly&nbsp;Basmati334.basmati.ragoo_scaffold.fa</p> <p>&nbsp;</p> <p>Basmati334.basmati.ragoo_scaffold.repeatmasker.bed</p> <p>- Repetitive DNA coordinates for the&nbsp;assembly&nbsp;Basmati334.basmati.ragoo_scaffold.fa</p> <p>&nbsp;</p> <p>CONSEL.tar.gz</p> <p>- Files used for CONSEL analysis</p> <p>&nbsp; &nbsp;- Folder&nbsp;CONSEL/PHYLOGENY_TEST/ contains the input files for CONSEL</p> <p>&nbsp; &nbsp;- Folder&nbsp;CONSEL/CONSEL_RESULT/ contains the CONSEL test results</p> <p>&nbsp;</p> <p>DADI_ANALYSIS.tar.gz</p> <p>- Input file for dadi analysis and scripts used for dadi modeling</p> <p>&nbsp;</p> <p>DomSufid.sadri.not_scaffolded.fa</p> <p>- Polished genome assembly for Dom Sufid but not scaffolded.</p> <p>&nbsp;</p> <p>DomSufid.sadri.not_scaffolded.sorted.gff</p> <p>- Gene annotation for the assembly&nbsp;DomSufid.sadri.not_scaffolded.fa</p> <p>&nbsp;</p> <p>DomSufid.sadri.ragoo_scaffold.fa</p> <p>-&nbsp;Polished genome assembly for Dom Sufid and scaffolding with RaGOO using the Nipponbare RAPDB1.0 as reference genome.</p> <p>&nbsp;</p> <p>DomSufid.sadri.ragoo_scaffold.sorted.gff</p> <p>- Gene annotation for the assembly DomSufid.sadri.ragoo_scaffold.fa</p> <p>&nbsp;</p> <p>DomSufid.sadri.ragoo_scaffold.repeatmasker.bed</p> <p>- Repetitive DNA coordinates for the&nbsp;assembly&nbsp;DomSufid.sadri.ragoo_scaffold.fa</p> <p>&nbsp;</p> <p>Four_rice_population.vcf.gz</p> <p>- Filtered SNP VCF file used in the basmati population relationship with japonica and aus.</p> <p>&nbsp;</p> <p>MULTIZ_ALIGNMENT.tar.gz</p> <p>- Reference genome alignment using&nbsp;Nipponbare RAPDB1.0 as reference and aligning various Oryza de novo genome assemblies</p> <p>&nbsp;</p> <p>Multi_Oryza_gene_FASTAs.tar.gz</p> <p>- Using the alignments from MULTIZ_ALIGNMENT/ pulled out coding DNA sequences of each&nbsp;Nipponbare RAPDB1.0 gene</p> <p>&nbsp;</p> <p>Obarthii_outgroup_AlignedToBasmatiScaffolded_genome.fa</p> <p>-&nbsp;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&nbsp;sequence resulting in a basmati-ized&nbsp;O. barthii&nbsp;genome sequence. Not alignable regions were indicated as &#39;N&#39;.&nbsp;</p> <p>&nbsp;</p> <p>Only_basmati_rice_population.vcf.gz</p> <p>-&nbsp;Filtered SNP VCF file used in the basmati population analysis.</p> <p>&nbsp;</p> <p>Oryza_LTR_DivergenceTime.txt</p> <p>- LTR retrotransposon annotated in various Oryza reference genomes and their estimated insertion time (based on the divergence between the LTRs).</p> <p>&nbsp;</p> <p>TWISST.tar.gz&nbsp;</p> <p>- TWISST input and results file.</p> <p>&nbsp; &nbsp;-&nbsp;Four_rice_population.geno.gz, genotype file generated from the genomic_general from S. Martin and used as input for TWISST analysis.</p> <p>&nbsp; &nbsp;- *.trees.gz phylogenetic trees generated from sliding windows</p> <p>&nbsp; &nbsp;- *.data.tsv sliding window coordinates</p> <p>&nbsp; &nbsp;- *.weights.csv.gz topology weights</p> <p>&nbsp;</p>