TomatoSuperPanGenome
Here, we sequence and de novo assemble chromosome-scale genomes of nine wild species and two cultivated accessions of tomato and constructed a pan-genome, revealing phylogenetic relationships and structural variation among Lycopersicon
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Download Latest Version (.zip)- 01_trinity_pasa.sh
- 02_denovo_prediction.sh
- 03_transcriptome.sh
- 04_homology.sh
- 05_evm.sh
- change_pos_snap.py
- changezff2oneline.py
- convert_genemarkGff3_2_EVMGff3.py
- eachgff2zff.py
- extrac_ok_gene.py
- extract_each_seq.py
- filter_ann.py
- format_trans.py
- glimmer_format.py
- ReadMe
- remove_trinity_GG.py
- split_glimmer.py
- weights.txt
- ReadMe
- repeat_annotation.sh
- ReadMe
- align_bnx_to_cmap.py
- bionano.sh
- fa2cmap_multi_color.pl
- hybridScaffold.pl
- hybridScaffold_config.xml
- optArguments_nonhaplotype_noES_noCut_BG_saphyr.xml
- pipelineCL.py
- ReadMe
- busco.sh
- ReadMe
- 01_hic-pro.sh
- 02_lachesis.sh
- convertHiCProMatrix2ordering.v2.pl
- CreateScaffoldedFasta.pl
- heatmap.MWAH.R
- lachesisGreedy.pl
- lachesisReport.pl
- out_len.py
- PreprocessSAMs.pl
- ReadMe
- retain_only_chr.py
- runLachesis.pl
- pilon.sh
- ReadMe
- canu.sh
- ReadMe
- PacBio mapping.sh
- plot_depth.R
- ReadMe
- ReadMe
- 1-nitro-2-phenylethane.txt
- 1-nitro-2-phenylethane.txt.xls
- 1-octen-3-one.txt
- 1-octen-3-one.txt.xls
- 1-penten-3-one.txt
- 1-penten-3-one.txt.xls
- 2-isobutylthiazole.txt
- 2-isobutylthiazole.txt.xls
- 2-methyl-1-butanol.txt
- 2-methyl-1-butanol.txt.xls
- 2-methylbutanal.txt
- 2-methylbutanal.txt.xls
- 2-phenylethanol.txt
- 2-phenylethanol.txt.xls
- 3-methyl-1-butanol.txt
- 3-methyl-1-butanol.txt.xls
- 6-methyl-5-hepten-2-one.txt
- 6-methyl-5-hepten-2-one.txt.xls
- Beta-ionone.txt
- Beta-ionone.txt.xls
- Citrate.txt
- Citrate.txt.xls
- E,E-2,4-decadienal.txt
- E,E-2,4-decadienal.txt.xls
- E-2-heptenal.txt
- E-2-heptenal.txt.xls
- E-2-hexenal.txt
- E-2-hexenal.txt.xls
- E-2-pentenal.txt
- E-2-pentenal.txt.xls
- Fructose.txt
- Fructose.txt.xls
- Geranylacetone.txt
- Geranylacetone.txt.xls
- Glucose.txt
- Glucose.txt.xls
- Guaiacol.txt
- Guaiacol.txt.xls
- Hexanal.txt
- Hexanal.txt.xls
- Hexylalcohol.txt
- Hexylalcohol.txt.xls
- Isobutylacetate.txt
- Isobutylacetate.txt.xls
- Isovaleraldehyde.txt
- Isovaleraldehyde.txt.xls
- Isovaleric_acid.txt
- Isovaleric_acid.txt.xls
- Isovaleronitrile.txt
- Isovaleronitrile.txt.xls
- Malate.txt
- Malate.txt.xls
- Methional.txt
- Methional.txt.xls
- Methylsalicylate.txt
- Methylsalicylate.txt.xls
- Phenylacetaldehyde.txt
- Phenylacetaldehyde.txt.xls
- SSC.txt
- SSC.txt.xls
- Z-3-hexen-1-ol.txt
- Z-3-hexen-1-ol.txt.xls
- Z-3-hexenal.txt
- Z-3-hexenal.txt.xls
- extract GWAS signals.sh
- find_sv_snpGWAS_overlap_uniq_signals_emmax.py
- GWAS.sh
- manhattan_qq.R
- output_peak_lead_SV.py
- ReadMe
- 362_annotated_metabolite_321_sample_phenotype.xls
- 362_annotated_metabolite_ID_name_corres.xls
- count GWAS peaks for Zhu et al.sh
- count_8classes_metabolites_peak.py
- GWAS.sh
- manhattan_qq.R
- output_peak_lead_SV.py
- plot_each_chromosome.R
- ReadMe
- ReadMe
- graph genome construction.sh
- ReadMe
- vg_vcf_head.xls
- filter_vcf_ad.py
- genotyped SV merge.sh
- ReadMe
- remove_duplicated_sites_in_vcf.py
- ReadMe
- convert_orthogroup_2_pan_matrix.py
- pan_genome.sh
- ReadMe
- baseml.ctl
- divergence time.sh
- mcmctree.usedata2.ctl
- mcmctree.usedata3.ctl
- ReadMe
- fa2phy.py
- phylogeny.sh
- ReadMe
- ReadMe
- 01_SyRI SV.sh
- 02_SVMU SV.sh
- 03_SNP INDEL.sh
- filter_delta_based_svmu_cm.py
- MUMmerSNPs2VCF.py
- output_chr_fasta.py
- output_translocation_from_vcf.py
- ReadMe
- uniq_vcf_chr_pos.py
- 01_INS DEL INV TRANS merge.sh
- 02_CNV merge.sh
- 12_sol_head
- add_cnv_id.py
- correct_identical_reference_pos_indel.py
- head_12
- merge_vcf.py
- ReadMe
- remove_problematic_indel_in_vcf.py
- go.R
- go_enrichment.sh
- merged_INS_DEL_wild_our_unique_impacted_genes.xls
- output_go_ipr_from_annot.py
- ReadMe
- S_galapagense.pos.go.ipr.txt
- 01_align_sv_from_heinz_2_GAL.sh
- 02_convert_sv_coordinates.sh
- filter_coords.py
- ReadMe
- remove_hezin_zy56_sv_varints.py
- convert_12_sol_100_cell_vcf.py
- filter_no_wild_SV.py
- merge.sh
- output_exon_gene.py
- output_work2_shell_CNV.py
- output_work2_shell_DEL.py
- output_work2_shell_INS.py
- output_work2_shell_INV.py
- ReadMe
- revise_merge_vcf_CHROM.py
- revise_vcf_GT1.py
- revise_vcf_GT2.py
- ReadMe
- ReadMe
- README.md
// repository documentation
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