Index of /public/dataset/HG002-CpG-methylation-202202

Icon  Name                                Last modified      Size  Description
[PARENTDIR] Parent Directory                                         -   
[   ] HG002.GRCh38.haplotagged.bam        2022-02-04 08:23   86G  
[   ] m64012_190920_173625.hifi_reads.bam 2022-02-04 08:37   22G  
[   ] m64012_190921_234837.hifi_reads.bam 2022-02-04 08:44   22G  
[   ] m64011_190830_220126.hifi_reads.bam 2022-02-04 08:29   21G  
[   ] m64011_190901_095311.hifi_reads.bam 2022-02-04 08:33   21G  
[   ] HG002.GRCh38.haplotagged.bam.bai    2022-02-04 11:49   17M  
[TXT] README.txt                          2022-02-04 07:12  933   
[TXT] MD5.txt                             2022-02-04 13:40  449   

OVERVIEW
    PacBio HiFi reads for HG002/NA24385 from the Human Pangenome Reference
    Consortium HG002 Data Freeze v1.0. Reads are tagged by haplotype (HP tag)
    and annotated with CpG methylation status (Mm and Ml tags).

    [1] https://github.com/human-pangenomics/HG002_Data_Freeze_v1.0
    [2] https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA586863


METHODS
    SHEARING         Megaruptor 3 to target size of 20 kb
    LIBRARY PREP     SMRTbell Express Template Prep Kit 2.0
    SIZE SELECTION   SageELF 15 kb and 20 kb fractions
    SEQUENCING       Sequel II System, 30 hr movie, Sequel II Chemistry 2.0
    ANALYSIS         Generate HiFi reads with ccs v6.0.0 with `--all-kinetics`
                     Add CpG methylation annotation with primrose v1.0.0
                     Align to GRCh38_no_alt_analysis_set with pbmm2 v1.4.0
                     Call variants with DeepVariant 1.0.0 and phase with whatshap 1.0