Microbial Multiplexing Data Set: PacBio Sequel System, Chemistry v3.0, SMRT Link v6.0.0 Analysis - PacificBiosciences/DevNet GitHub Wiki
This is SMRT Sequencing data for a 10-plex multiplexed data set using the Barcoded Overhang Adapter 8A and Barcoded Overhang Adapter 8B kits complementing the SMRTbell Express Template Prep Kit 2.0. The pooled library contains a total of 42.4 Mb microbial genomes from different samples and has been sequenced on a single SMRT Cell.
The libraries include two PacBio control microbes and customer samples. Sequencing was performed on the Sequel System using Binding/Sequencing Chemistry v3.0 and analyzed with HGAP4 in SMRT Link v6.0.0. Assembled genomes have been circularized using the Circlator tool and polished through the Resequencing analysis on SMRT Link.
This data set accompanies Application Note: Microbial Multiplexing Workflow on the Sequel System using the SMRTbell Express Template Prep Kit 2.0, which details key considerations for experimental design and practices on the Sequel System.
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DATA SETS and supporting files (11 files):
BC1001_Escherichia_coli_str_K-12_substr_MG1655.Lucigen.HGAP_polish.fasta - Final polished genome assembly for E. coli multiplexed using barcoded adapter BC1001.
BC1002_Escherichia_coli_str_K-12_substr_MG1655.Circulomics.HGAP_polish.fasta - Final polished genome assembly for E. coli multiplexed using barcoded adapter BC1002.
BC1009_Klebsiella_pneumoniae_str_ATCC_BAA-2146.HGAP_polish.fasta- Final polished genome assembly for K. pneumoniae multiplexed using barcoded adapter BC1009.
BC1010_Bacillus_cereus_ATCC_14579.HGAP_polish.fasta - Final polished genome assembly for B. cereus multiplexed using barcoded adapter BC1010.
BC1012_Listeria_monocytogenes_str_CFSAN008100.HGAP_polish.fasta - Final polished genome assembly for L. monocytogenes multiplexed using barcoded adapter BC1012.
BC1015_Shigella_sonnei_str_CFSAN030807.HGAP_polish.fasta - Final polished genome assembly for S. sonnei multiplexed using barcoded adapter BC1015.
BC1016_Neisseria_meningitidis_FAM18.HGAP_polish.fasta - Final polished genome assembly for N. meningitidis multiplexed using barcoded adapter BC1016.
BC1018_Staphylococcus_aureus_subsp_aureus_str_ATCC_25923.HGAP_polish.fasta - Final polished genome assembly for S. aureus multiplexed using barcoded adapter BC1018.
BC1019_Escherichia_coli_W_ATCC_9637.HGAP_polish.fasta - Final polished genome assembly for E. coli W multiplexed using barcoded adapter BC1019.
BC1022_Staphylococcus_aureus_HPV107.HGAP_polish.fasta - Final polished genome assembly for S. aureus HPV107 multiplexed using barcoded adapter BC1022.
MM_10Plex_42MB_SEQUENCING_DATA_EXPRESS2.0.tar.gz - Compressed gzipped file containing BAM file for original sequencing data and supporting .pbi and .xml files for importing into SMRT Link.
We provide final genome assemblies that have been twice polished with the Resequencing module and circularized with Circlator for all microbes except Listeria monocytogenes. For Listeria_monocytogenes, final polished HGAP4 genome is provided since we’ve found Circlator integrated the plasmid into the main chromosomal assembly.
DNA was extracted using the Circulomics Nanobind CBB Big DNA Kit for BC1002, BC1009, BC1010, BC1012, BC1015, BC1016, BC1018, BC1019, BC1022. The Lucigen MasterPure Complete DNA and RNA Purification Kit was used to extract the PacBio Controls (BC1001).