Index of /public/dataset/2021-11-Microbial-96plex

Icon  Name                    Last modified      Size  Description
[PARENTDIR] Parent Directory                             -   
[DIR] reads/                  2021-11-10 11:10    -   
[DIR] demultiplexed-reads/    2021-11-10 11:10    -   
[DIR] asms/                   2021-11-10 11:12    -   
[TXT] README.txt              2021-11-11 00:27  3.6K  

SAMPLES

    MICROBE                                    CHROMOSOME SIZES (Mb)  PLASMID SIZES (kb)    BARCODES
    -------                                    ---------------------  ------------------    ---------------------------
    Acinetobacter baumannii AYE                3.9                    9.7; 5.6; 2.7         bc2001,bc2025,bc2049,bc2073
    Bacillus cereus 971                        5.4                    15.2                  bc2002,bc2026,bc2050,bc2074
    Bacillus subtilis W23                      4                      -                     bc2003,bc2027,bc2051,bc2075
    Burkholderia cepacia UCB 717               3.8; 3.4; 1.2          204                   bc2004,bc2028,bc2052,bc2076
    Burkholderia multivorans 249               3.4; 2.5; 0.92         167                   bc2005,bc2029,bc2053,bc2077
    Enterococcus faecalis OG1RF                2.7                    -                     bc2006,bc2030,bc2054,bc2078
    Escherichia coli H10407                    5.2                    95; 68; 67; 5.8; 5.5  bc2007,bc2031,bc2055,bc2079
    Escherichia coli K12 MG1655                4.6                    -                     bc2008,bc2032,bc2056,bc2080
    Helicobacter pylori J99                    1.6                    -                     bc2009,bc2033,bc2057,bc2081
    Klebsiella pneumoniae BAA-2146             5.4                    141; 118; 84; 2       bc2010,bc2034,bc2058,bc2082
    Listeria monocytogenes Li2                 3                      -                     bc2011,bc2035,bc2059,bc2083
    Listeria monocytogenes Li23                3                      -                     bc2012,bc2036,bc2060,bc2084
    Methanocorpusculum labreanum Z             1.8                    -                     bc2013,bc2037,bc2061,bc2085
    Neisseria meningitidis FAM18               2.2                    -                     bc2014,bc2038,bc2062,bc2086
    Neisseria meningitidis Serogroup B         2.3                    -                     bc2015,bc2039,bc2063,bc2087
    Rhodopseudomonas palustris CGA009          5.4                    8.4                   bc2016,bc2040,bc2064,bc2088
    Salmonella enterica LT2                    4.9                    93.9                  bc2017,bc2041,bc2065,bc2089
    Salmonella enterica Ty2                    4.8                    -                     bc2018,bc2042,bc2066,bc2090
    Staphylococcus aureus Seattle 1945         2.7; 0.07              27.5                  bc2019,bc2043,bc2067,bc2091
    Staphylococcus aureus USA300 TCH1516       2.9                    28; 2                 bc2020,bc2044,bc2068,bc2092
    Streptococcus pyogenes Bruno               1.8                    -                     bc2021,bc2045,bc2069,bc2093
    Thermanaerovibrio acidaminovorans DSM6589  1.9                    -                     bc2022,bc2046,bc2070,bc2094
    Treponema denticola A                      2.8                    -                     bc2023,bc2047,bc2071,bc2095
    Vibrio parahaemolyticus EB101              3.3; 1.9               -                     bc2024,bc2048,bc2072,bc2096


METHODS

    96 libraries were prepared, 4 replicates per sample for each of 24 samples.

    INPUT       1 µg / sample
    SHEARING    Megaruptor 3 at speed 40
    BARCODING   SMRTbell Barcoded Adapter Plate 3.0 (102-009-200)
    SEQUENCING  Sequel II System, 15 hr movie, 2 hr pre-extension, 0.85 adaptive loading target
    ANALYSIS    Generate HiFi reads with ccs v6.2.0, including `--hifi-kinetics`
                Demultiplex with lima v2.3.99: `lima --split-named --preset HIFI-SYMMETRIC --single-side`
                Assemble with HiFi Microbial Assembly application in SMRT Link 10.2 using default parameters