This folder contains the data necessary for the analysis described in GrAnnoT's paper (doi), and the files produced with this data. The command lines used to process this data and produce the outputs are described in the file "grannot_analysis_command_lines.txt". The only unprovided data are the 12 genomes sequences, issued from the paper from 2020 by Zhou, Y., Chebotarov, D., Kudrna, D. et al., "A platinum standard pan-genome resource that represents the population structure of Asian rice" (doi:10.1038/s41597-020-0438-2). These genomes were used to build the rice pangenome graph (along with the Nipponbare reference (doi:10.1186/1939-8433-6-4)), and for the Liftoff transfers. The rice annotation comes from the Rice Genome Annotation Project, available at https://rice.uga.edu/ The E.coli genomes used to build the pangenome graph come from the paper available at http://dx.doi.org/10.7554/eLife.78834 The K12_MG1655 annotation is adapted from : https://www.ncbi.nlm.nih.gov/nuccore/U00096.3 to match the pangenome graph. The graph was made by the Human Pangenome Reference Consortium, and is available at https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=pangenomes/scratch/2022_03_11_minigraph_cactus/ The human genomes for the Liftoff transfer come from https://projects.ensembl.org/hprc/ The CHM13 annotation is adapted from : https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/ to match the pangenome graph. This folder is organised as such : . ├── data │   ├── ecoli │   │   ├── EcoliGraph_MGC.gfa │   │   ├── feature_types.txt │   │   ├── K_12_MG1655_09949b0.fasta │   │   ├── O127_H6_E2348_69_193637c.fasta │   │   └── sequence_filter_rename_K_12_MG1655_09949b0.gff3 │   ├── human │   │   ├── CHM13_chr1.gff │   │   ├── chm13.draft_v1.1_chr1.fasta │   │   ├── feature_types.txt │   │   ├── GCA_000001405.15_GRCh38_no_alt_analysis_set_chr1.fna │   │   └── HumanChr1Graph_renamePaths.gfa │   └── rice │   ├── GCA_009830595.1_AzucenaRS1_genomic.fna │ ├── nb_allFeatures.fa │   ├── nb_allFeatures.gff3 │   ├── nb_allFeatures_renamed_filter.bed │   ├── nb_allFeatures_renamepath_annotate.gff3 │   ├── refpath_odgi │   ├── refpath_vg │   ├── RiceGraph_MGC.gfa │   ├── RiceGraph_MGC_paths.gfa │   ├── RiceGraph_MGC_refOs127652RS1.gfa │   ├── TIGRv7_ok.fasta │   └── TIGRv7_ok.genome ├── grannot_analysis_command_lines.txt ├── outputs │   ├── ecoli │   │   ├── intermediate_files │   │   │   ├── reference_all_genes.fa │   │   │   └── reference_all_to_target_all.sam │   │   ├── liftoff_transfer_k12_to_0127.gff │   │   ├── O127_H6_E2348_69_193637c │   │   │   └── O127_H6_E2348_69_193637c.gff │   │   └── unmapped_features.txt │   ├── human │   │   ├── GRCh38 │   │   │   └── GRCh38.gff │   │   ├── intermediate_files │   │   │   ├── reference_all_genes.fa │   │   │   └── reference_all_to_target_all.sam │   │   ├── liftoff_transfer_chm13_to_grch38.gff │   │   └── unmapped_features.txt │   └── rice │   ├── back_forth_transfer │   │   ├── grannot │   │   │   ├── AzucenaRS1.gff │   │   │   └── IRGSP.gff │   │   └── liftoff │   │   ├── AzucenaRS1.gff3 │   │   └── IRGSP.gff3 │   ├── grannot │   │   ├── AzucenaRS1 │   │   │   ├── AzucenaRS1.gff │   │   │   ├── AzucenaRS1_var_sorted.txt │   │   │   └── AzucenaRS1_var.txt │ │ ├── AzucenaRS1_refOs127652RS1.gff │ │ ├── RiceGraph_MGC.gaf │   │   └── segments.txt │   ├── grannot_multi │   │   ├── AzucenaRS1 │   │   │   └── AzucenaRS1.gff │   │   ├── Os117425RS1 │   │   │   └── Os117425RS1.gff │   │   ├── etc... │   │   └── PAV_matrix.txt │ ├── graphaligner │ │   └── graphaligner_rice_transfer.gaf │   ├── liftoff_multi │   │   ├── AzucenaRS1_named.db.gff │   │   ├── AzucenaRS1_named.gff │   │   ├── AzucenaRS1_named_unmappeddb.txt │   │   ├── AzucenaRS1_named_unmapped.txt │   │   ├── Os117425RS1_named.db.gff │   │   ├── Os117425RS1_named.gff │   │   ├── Os117425RS1_named_unmappeddb.txt │   │   ├── Os117425RS1_named_unmapped.txt │   │   └── etc... │   ├── odgi │   │   └── odgi_transfer_nb_azu.bed │   └── vg │   ├── nb_allFeatures_annotate.gaf │   ├── nb_allFeatures_annotate.gam │   ├── nb_allFeatures_renamed_filter.bam │   ├── nb_allFeatures_renamed_filter.gaf │   ├── nb_allFeatures_renamed_filter.sam │   └── RiceGraph_MGC_paths.xg └── readme.txt