Index of /public/revio/2022Q4

 Name                           Last modified      Size  Description
 Parent Directory                                    -   
 dv-model/                      2022-12-26 14:31    -   
 WGS-variant-pipeline-analysis/ 2023-11-13 11:03    -   
 HG004-rep1/                    2023-04-12 12:50    -   
 HG003-rep1/                    2022-12-26 22:32    -   
 HG002-rep3/                    2022-12-26 22:32    -   
 HG002-rep2/                    2022-12-26 22:32    -   
 HG002-rep1/                    2022-12-26 22:32    -   
 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