SAMPLES

    SAMPLE                                  PROTOCOL    BARCODE PAIR NAME
    ------                                  --------    -------
    Fecal reference (Zymo D6323)            WGS         bc2001
    Fecal reference (Zymo D6323)            Ampli-Fi    Plate_A_1_A01
    Gut microbiome standard (Zymo D6331)    WGS         bc2002
    Gut microbiome standard (Zymo D6331)    Ampli-Fi    Plate_A_2_B01


METAGENOMIC SAMPLE POOL PREPARED WITH AMPLI-FI PROTOCOL AND WGS PROTOCOL
METHODS
    4 libraries were prepared: fecal reference (Zymo D6323) and gut microbiome standard (Zymo D6331) using both the Ampli-Fi protocol and WGS protocol for each sample
    PROTOCOL    Amplifying genomic DNA for SMRTbell library preparation and HiFi sequencing (103-648-000 REV2 MAR2025)
                Preparing whole genome and metagenome libraries using SMRTbell prep kit 3.0 (102-166-600 REV06 JAN2025)
    INPUT       Ampli-Fi protocol: 45 ng/sample
                WGS protocol: 2 ug/sample
    SHEARING    Not applicable: fecal reference stock sized at 10.1 kb and gut microbiome standard stock sized at 7.4 kb 
    BARCODING   Ampli-Fi protocol: Twist Universal Adapter System TruSeq Compatible, 96 Samples Plate A (101308)
                WGS protocol: SMRTbell adapter index plate 96A (102-009-200)
    SEQUENCING  Vega system, 200 pM loading concentration, 24 hr movie (m21015_250606_023823)
                Revio system, 225 pM loading concentration, 24 hr movie (m84039_250606_030410_s4)
    ANALYSIS    WGS Protocol:
                    Demultiplex SMRTbell adapters with lima v2.12.0: `lima --split-bam-named --preset SYMMETRIC-ADAPTERS`
                Ampli-Fi Protocol:
                    Demultiplex Twist UDI adapters with lima v2.12.0: `lima --split-bam-named --preset ASYMMETRIC`
                    Remove PCR duplicates with pbmarkdup v1.1.0: `pbmarkdup --hifi --remove-pcr-duplicates`