Hak-Min Kim KOREF

KOREF

 

1. Raw data and project folder information

1. Project folder:
   1. KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/
   2. KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/
2. Raw data information: http://in.tgi.kr/index.php/Overall_Data_Information

 

2. Paper status: Published (An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nature communications, 2016)

 

3. Analysis result

1. Assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly
2. Annotation result (Gene set / Repeat): KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Annotation
   1. Ethnic gene prediction result: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit
   2. Ethnic repeat masking result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask
3. Mitochondria assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Mitochondria_assembly
4. Ethnic assemblies segmental duplication result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/SegmentalDuplication

 

4. Related script

1. Repeat maksing
   1. Run repeat masking: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/0_RepeatMasking_the_genome.pl
   2. Count the hetero variants in repeat region: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/1_Count_hetero_variants_in_repeat_region_withArray.pl
2. Sspace_longread (scaffolding program)
   1. Run Sspace_longread with Pacbio and Moleculo data: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly/3.Pacbio_Moleculo_SSPACE_with_2/script/0_SSPACE-longread_run_with_Pacbio_Moleculo.pl
3. Exonerate unmapped count script: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit/Exonerate_unmpped_count.pl

 

5. Methods

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