OVERVIEW

This directory includes three human HG002 WGS datasets produced with the Ampli-Fi protocol. Each dataset represents a different DNA polymerase used to amplify the same sheared genomic DNA. Libraries were sequenced using SPRQ chemistry, one acquisition per SMRT Cell. 

METHODS
    SHEARING        Megaruptor 3 shearing to an average insert size of 11 kb
    AMPLIFICATION   Twist universal adapters were ligated to sheared DNA and amplified with one of three DNA polymerases: 
                        KURA Biotech DeCodi Long & Complex 2X All-in-One Mix, no part number
                        Millipore Sigma KOD Xtreme Hot Start DNA Polymerase, 71975-3
                        Takara Bio PrimerSTAR LongSeq DNA Polymerase, R055A
    LIBRARY PREP    Ampli-Fi protocol using Twist Bioscience Universal Adapter system and primers and SMRTbell prep kit 3.0 
    SEQUENCING      Revio system, SPRQ chemistry, 24-hour acquisition 
    ANALYSIS        On-instrument base calling. Secondary analysis tools for demultiplexing, removing PCR duplicates, and mapping reads to the HG002 T2T v1.0.1 reference. The HiFi-human-assembly-WDL pipeline was used for assembly. 

DIRECTORIES
    decodifi_long_and_complex   Dataset amplified with the DeCodi-Fi Long & Complex 2x All-in-One Mix 
    kod_xtreme_hs               Dataset amplified with the KOD Xtreme Hot Start DNA Polymerase
    primestar_longseq           Dataset amplified with PrimeSTAR LongSeq DNA polymerase

SUBDIRECTORIES 
    aligned_reads   Demultiplexed and deduplicated reads aligned to the HG002 T2Tv1.0.1 reference
    assembly        Assembly of the HIFI READS using the HiFi-human-assembly-WDL v1.0.2 pipeline
    hifi_reads      Demultiplexed and deduplicated reads