Darmor Tapidor

This page collects the files for Bayer et al. B. napus Darmor/Tapidor genome paper

Software

Collinearity analysis - parses MCScanX results and checks for missing genes in expected regions Collinearity_scripts.zip

LASTZSorter.py - sorts contigs based on LASTZ alignment with reference LASTZSorter.py

contigPlacer - places contigs based on recombination patterns contigPlacer

R-scripts used for plotting - Venn-diagrams, boxplots R_plotting_scripts.zip

The SkimGBS pipeline is available here: http://appliedbioinformatics.com.au/index.php/SkimGBS

Results

Tapidor genetic map from MSTMap (txt)

Darmor SNPs anchored on Darmor v8.1 reference (gff3)

Tapidor SNPs anchored on Tapidor v6.3 reference (gff3)

List of genes in repetitive and collapsed regions

Coordinates of repetitive and collapsed regions in Darmor and Tapidor

Pfam and Swissprot results for repetitive and collapsed genes

Annotation

List of Transposase related PFAM IDs used for filtering

GO_Arabidopsis_Terms.zip Swiss-Prot/Arabidopsis based GO terms for Darmor and Tapidor annotation

Tapidor

Tapidor_v63_assembly.fasta.gz - assembly as pseudo-molecules

Tapidor_v6.3_contig_order.zip - contig positions in assembly as gff3

Filtered annotation

No AED=1 scores, transcripts longer than 100 bp, no Transposase domains

Tapidor_v63_assembly.augustus_masked_filtered.gff.gz - filtered predicted annotation in GFF format

Tapidor_v63_assembly.all.maker.augustus_masked.transcripts_filtered.fasta.gz - filtered predicted transcripts

Tapidor_v63_assembly.all.maker.augustus_masked.proteins_filtered.fasta.gz - filtered predicted proteins

Tapidor_v63_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz - PFam results for filtered predicted proteins

Darmor

Darmor_v81_assembly_fasta.gz - assembly as pseudomolecules

Darmor_v8.1_contig_order.zip - order of contigs as gff3 files

Filtered annotation

No AED=1 scores, transcripts longer than 100 bp, no Transposase domains

Darmor_v81_assembly.augustus_masked_filtered.gff.gz - filtered predicted annotation in GFF format

Darmor_v81_assembly.all.maker.augustus_masked.transcripts_filtered.fasta.gz - filtered predicted transcripts

Darmor_v81_assembly.all.maker.augustus_masked.proteins_filtered.fasta.gz - filtered predicted proteins

Darmor_v81_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz - PFam results for filtered predicted proteins