Index of /public/revio/2025Q2/microbes/isolates-vega
SAMPLES
TAXONOMIC NAME ATCC STRAIN NAME CONTIG SIZES BARCODE PAIR NAME
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Acinetobacter baumannii AYE ATCC BAA-1710 3.9M, 9.7k, 5.6k, 2.7k Plate_A_1_A01,Plate_A_2_B01,Plate_A_3_C01,Plate_A_4_D01,Plate_A_5_E01,Plate_A_6_F01
Campylobacter jejuni subsp. jejuni CIP 702 ATCC 33560 1.8M Plate_A_7_G01,Plate_A_8_H01,Plate_A_9_A02,Plate_A_10_B02,Plate_A_11_C02,Plate_A_12_D02
Clostridium perfringens ATCC 13124 3.3M Plate_A_13_E02,Plate_A_14_F02,Plate_A_15_G02,Plate_A_16_H02,Plate_A_17_A03,Plate_A_18_B03
Cronobacter sakazakii 2001-10-01 ATCC BAA-894 4.3M, 131.2k, 31.2k, 2.7k Plate_A_19_C03,Plate_A_20_D03,Plate_A_21_E03,Plate_A_22_F03,Plate_A_23_G03,Plate_A_24_H03
Enterobacter cloacae subsp. cloacae CDC 442-68 ATCC 13047 5.3M, 199.6k, 86.3k, 5.1k Plate_A_25_A04,Plate_A_26_B04,Plate_A_27_C04,Plate_A_28_D04,Plate_A_29_E04,Plate_A_30_F04
Enterococcus faecium MMC4 ATCC 51559 2.8M, 215.9k, 63.7k, 43.0k, 12.5k, 4.4k, 2.9k, 2.0k Plate_A_31_G04,Plate_A_32_H04,Plate_A_33_A05,Plate_A_34_B05,Plate_A_35_C05,Plate_A_36_D05
Escherichia coli MG1655 ATCC 700926 4.6M Plate_A_37_E05,Plate_A_38_F05,Plate_A_39_G05,Plate_A_40_H05,Plate_A_41_A06,Plate_A_42_B06
Escherichia coli H10407 ATCC 35401 5.2M, 94.8k, 67.9k, 66.6k, 5.8k, 5.5k Plate_A_43_C06,Plate_A_44_D06,Plate_A_45_E06,Plate_A_46_F06,Plate_A_47_G06,Plate_A_48_H06
Klebsiella pneumoniae 1000527, 7561 ATCC BAA-2146 5.4M, 140.8k, 117.8k, 84.4k, 2.0k Plate_A_49_A07,Plate_A_50_B07,Plate_A_51_C07,Plate_A_52_D07,Plate_A_53_E07,Plate_A_54_F07
Listeria monocytogenes Li 2 ATCC 19115 3.0M Plate_A_55_G07,Plate_A_56_H07,Plate_A_57_A08,Plate_A_58_B08,Plate_A_59_C08,Plate_A_60_D08
Pseudomonas aeruginosa PAO1-LAC ATCC 47085 6.3M, 12.3k, 11.7k Plate_A_61_E08,Plate_A_62_F08,Plate_A_63_G08,Plate_A_64_H08,Plate_A_65_A09,Plate_A_66_B09
Salmonella enterica subsp. Enterica serovar Typhimurium LT2 ATCC 700720 4.9M, 93.9k Plate_A_67_C09,Plate_A_68_D09,Plate_A_69_E09,Plate_A_70_F09,Plate_A_71_G09,Plate_A_72_H09
Shigella flexneri 2457T ATCC 700930 4.6M, 165.7k, 4.1k, 3.2k Plate_A_73_A10,Plate_A_74_B10,Plate_A_75_C10,Plate_A_76_D10,Plate_A_77_E10,Plate_A_78_F10
Staphylococcus aureus subsp. aureus Seattle 1945 ATCC 25923 2.8M, 27.5k Plate_A_79_G10,Plate_A_80_H10,Plate_A_81_A11,Plate_A_82_B11,Plate_A_83_C11,Plate_A_84_D11
Vibrio campbellii BB120 ATCC BAA-1116 3.8M, 2.2M, 89.0k Plate_A_85_E11,Plate_A_86_F11,Plate_A_87_G11,Plate_A_88_H11,Plate_A_89_A12,Plate_A_90_B12
Vibrio parahaemolyticus EB101 ATCC 17802 3.3M, 1.9M Plate_A_91_C12,Plate_A_92_D12,Plate_A_93_E12,Plate_A_94_F12,Plate_A_95_G12,Plate_A_96_H12
ISOLATE SAMPLE POOL PREPARED WITH AMPLI-FI PROTOCOL
METHODS
96 libraries were prepared: 6 replicates per sample for each of 16 samples
PROTOCOL Amplifying genomic DNA for SMRTbell library preparation and HiFi sequencing (103-648-000 REV2 MAR2025)
INPUT 45 ng/sample
SHEARING Covaris g-TUBE, 400 ng in 65 uL total low-EDTA TE, 5 min at 3,000 x g
BARCODING Twist Universal Adapter System TruSeq Compatible, 96 Samples Plate A (101308)
SEQUENCING Vega system, 200 pM loading concentration, 24 hr movie (m21020_250606_024001)
ANALYSIS 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`