Hak-Min Kim KOREF
From kogic.kr
KOREF
1. Raw data and project folder information
- Project folder:
- KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/
- KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/
- 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
- Assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly
- Annotation result (Gene set / Repeat): KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Annotation
- Ethnic gene prediction result: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit
- Ethnic repeat masking result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask
- Mitochondria assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Mitochondria_assembly
- Ethnic assemblies segmental duplication result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/SegmentalDuplication
4. Related script
- Repeat maksing
- Run repeat masking: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/0_RepeatMasking_the_genome.pl
- 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
- Sspace_longread (scaffolding program)
- 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
- Exonerate unmapped count script: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit/Exonerate_unmpped_count.pl
5. Methods
- Assembly process
- All methods are described in the method & material section of the published article.
