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) - MSTMap_Input.zip Input file for MSTMap

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

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

Repetitive_Collapsed_Genes.zip List of genes in repetitive and collapsed regions

Repetitive_Collapsed_Regions.zip Coordinates of repetitive and collapsed regions in Darmor and Tapidor (bed)

SwissProt_Pfam_hits_Repetitive_Collapsed_Genes.zip 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 v6.3

Tapidor_v63_assembly.fasta.gz - assembly as pseudo-molecules

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

Unfiltered annotation

Straight from AUGUSTUS, with MAKER's AED scores

Tapidor_v63_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz - annotation in GFF format

Tapidor_v63_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz - predicted proteins

Tapidor_v63_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz - predicted transcripts

Filtered annotation

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

Tapidor_v63_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz - filtered predicted annotation in GFF format

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

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

Darmor v8.1

Darmor_v81_assembly_fasta.gz - assembly as pseudo-molecules

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

Unfiltered annotation

Straight from AUGUSTUS, with MAKER's AED scores

Darmor_v81_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz - annotation in GFF format

Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz - proteins, fasta

Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz - transcripts, fasta

Filtered annotation

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

Darmor_v81_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz - filtered predicted annotation in GFF format

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

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