Hak-Min Kim Leopard

 

 

Leopard genome

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1. Raw data and project folder information

1. Project folder
   1. Whale서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03
2. Raw data information:
   1. Illumina short/mate reads: Whale서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/0.Rawdata
   2. Moleculo long reads: Whale서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/0.Rawdata/Moleculo

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2. Paper status: Published (Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly. Genome biology, 2016)

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3. Analysis result

1. Assembly result: /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/13.SNV_INDEL_substitution_scaffold/Amurleopard.K63.Gapclosed_SNV.INDEL.substituted.new.fa
2. Annotation result:
   1. Gene set (Paper version): /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/24.FinalGenes/Leopard
   2. Gene set (NCBI version):
      1. GFF: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/857/705/GCF_001857705.1_PanPar1.0/GCF_001857705.1_PanPar1.0_genomic.gff.gz
      2. Protein seq: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/857/705/GCF_001857705.1_PanPar1.0/GCF_001857705.1_PanPar1.0_protein.faa.gz
      3. CDS seq: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/857/705/GCF_001857705.1_PanPar1.0/GCF_001857705.1_PanPar1.0_translated_cds.faa.gz
3. Orthologous gene cluster & gene expansion and contraction: /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/25.Orthologous_gene_cluster_Input/OthoMCL_result_Tasmanian
4. Felidae species mapping result: /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/23.Multi-mapping-Felidae-species
5. Selective sweep (Highly conserved region): KOREF서버 /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/Seletive_sweep/Selective_sweep/Result_FamilyLevel
6. Pairwise sequentially Markovian coalescent analysis (PSMC): /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/Workspace/tgikimhh/PSMC

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4. Related script

1. Assembly refinement with Moleculo (Gap filling with moleculo)

It is composed of 6 scripts and plays the role of gap filling using Moleculo. Execute script 0 to 5 sequentially

1. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/0_mapping_moleculo_to_Amurleopard.pl
2. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/1_Covered_N_base_detect.pl
3. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/2_Extract_moleculo_reads_from_N_region.pl
4. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/3_Replace_scaffold_with_moleculo.pl
5. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/4_Substituted_N_count.pl
6. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/15.Moleculo_Align_with_substituted_scaffold_BWA/5_Scaffold_finalize.pl
7. Calculation Moleculo length and yield distribution
   1. /BiO/Research/Project1/TGI-AmurLeopard-Genome-2015-03/0.Rawdata/Moleculo/0_length_distribution_and_yield_distribution.pl

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5. Methods

1. All methods are described in the method & material section of the published article.