Index of /public/revio/2022Q4

Icon  Name                    Last modified      Size  Description
[PARENTDIR] Parent Directory - [DIR] HG002-rep1/ 2022-10-21 07:02 - [DIR] HG002-rep2/ 2022-10-21 07:02 - [DIR] HG002-rep3/ 2022-10-21 07:02 - [DIR] HG003-rep1/ 2022-10-21 07:02 - [DIR] HG004-rep1/ 2022-10-21 07:02 - [DIR] dv-model/ 2022-10-21 07:32 - [TXT] README.txt 2022-10-21 07:23 1.0K
OVERVIEW
    This directory includes human whole genome sequencing datasets from the
    Revio system for the Genome in a Bottle trio HG002+HG003+HG004, with one
    Revio SMRT Cell per sample replicate.


DIRECTORIES
    dv-model        DeepVariant model for Revio system
    HG002-rep1      HG002 replicate 1
    HG002-rep2      HG002 replicate 2
    HG002-rep3      HG002 replicate 3
    HG003-rep1      HG003 replicate 1
    HG004-rep1      HG004 replicate 1


METHODS
    SHEARING         Megaruptor 3 to target size of 15-20 kb
    LIBRARY PREP     SMRTbell prep kit 3.0
    SEQUENCING       Revio system, 24 hour movie
    ANALYSIS         Generate HiFi reads with methylation calls on the Revio system
                     Align to GRCh38_no_alt_analysis_set with pbmm2 v1.9.0
                     Call small variants with DeepVariant 1.4.0 using the Revio model
                     Phase small variants and haplotag reads with whatshap 1.4
                     Call structural variants with pbsv v2.8.0