Index of /public/dataset/microbial_multiplex_dataset_release_SMRT_Link_v6.0.0_with_Express_2.0

Icon  Name                                                                         Last modified      Size  Description
[PARENTDIR] Parent Directory - [TXT] README.txt 2019-02-26 11:06 4.5K [   ] BC1016_Neisseria_meningitidis_FAM18.HGAP_polish.fasta 2019-02-20 15:45 2.1M [   ] BC1018_Staphylococcus_aureus_subsp_aureus_str_ATCC_25923.HGAP_polish.fasta 2019-02-20 15:47 2.7M [   ] BC1022_Staphylococcus_aureus_HPV107.HGAP_polish.fasta 2019-02-20 15:46 2.9M [   ] BC1012_Listeria_monocytogenes_str_CFSAN008100.HGAP_polish.fasta 2019-02-20 15:45 3.0M [   ] BC1002_Escherichia_coli_str_K-12_substr_MG1655.Circulomics.HGAP_polish.fasta 2019-02-20 15:42 4.5M [   ] BC1001_Escherichia_coli_str_K-12_substr_MG1655.Lucigen.HGAP_polish.fasta 2019-02-20 15:43 4.5M [   ] BC1015_Shigella_sonnei_str_CFSAN030807.HGAP_polish.fasta 2019-02-20 15:46 4.7M [   ] BC1019_Escherichia_coli_W_ATCC_9637.HGAP_polish.fasta 2019-02-20 15:44 4.8M [   ] BC1010_Bacillus_cereus_ATCC_14579.HGAP_polish.fasta 2019-02-20 15:43 5.3M [   ] BC1009_Klebsiella_pneumoniae_str_ATCC_BAA-2146.HGAP_polish.fasta 2019-02-20 15:44 5.6M [   ] MM_10Plex_42MB_SEQUENCING_DATA_EXPRESS2.0.tar.gz 2019-02-20 16:30 31G
Last Updated:  February 21, 2019

This README file contains information for the SMRT Sequencing data from a 10-plex multiplexed dataset 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 using Binding/Sequencing chemistry 3.0 and analyzed with HGAP4 in SMRT Link v6.0.0.  Assembled genomes provided have been circularized using the Cirlator tool ( and polished through the Resequencing analysis job on SMRT Link.

This dataset 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 considerations for best outcomes on the Sequel System. (

DATASETS and supporting files (11 files):

1.	BC1001_Escherichia_coli_str_K-12_substr_MG1655.Lucigen.HGAP_polish.fasta - Final polished genome assembly for E. coli multiplexed using barcoded adapter BC1001.
2.	BC1002_Escherichia_coli_str_K-12_substr_MG1655.Circulomics.HGAP_polish.fasta - Final polished genome assembly for E. coli multiplexed using barcoded adapter BC1002.
3.	BC1009_Klebsiella_pneumoniae_str_ATCC_BAA-2146.HGAP_polish.fasta- Final polished genome assembly for K. pneumoniae multiplexed using barcoded adapter BC1009.
4.	BC1010_Bacillus_cereus_ATCC_14579.HGAP_polish.fasta - Final polished genome assembly for B. cereus multiplexed using barcoded adapter BC1010. 
5.	BC1012_Listeria_monocytogenes_str_CFSAN008100.HGAP_polish.fasta - Final polished genome assembly for L. monocytogenes multiplexed using barcoded adapter BC1012.
6.	BC1015_Shigella_sonnei_str_CFSAN030807.HGAP_polish.fasta - Final polished genome assembly for S. sonnei multiplexed using barcoded adapter BC1015.
7.	BC1016_Neisseria_meningitidis_FAM18.HGAP_polish.fasta - Final polished genome assembly for N. meningitidis multiplexed using barcoded adapter BC1016.
8.	BC1018_Staphylococcus_aureus_subsp_aureus_str_ATCC_25923.HGAP_polish.fasta - Final polished genome assembly for S. aureus multiplexed using barcoded adapter BC1018.
9.	BC1019_Escherichia_coli_W_ATCC_9637.HGAP_polish.fasta - Final polished genome assembly for E. coli W multiplexed using barcoded adapter BC1019.
10.	BC1022_Staphylococcus_aureus_HPV107.HGAP_polish.fasta - Final polished genome assembly for S. aureus HPV107 multiplexed using barcoded adapter BC1022.
11.	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).

For Research Use Only. Not for use in diagnostic procedures.  Copyright 2019, Pacific Biosciences of California, Inc. All rights reserved. The data provided in these files is subject to change without notice and Pacific Biosciences assumes no responsibility for any errors or omissions. Certain notices, terms, conditions and/or use restrictions may pertain to your use of Pacific Biosciences data, products and/or third party products. Please refer to the applicable Pacific Biosciences Terms and Conditions of Sale and to the applicable license terms at Pacific Biosciences, the Pacific Biosciences logo, PacBio, SMRT, SMRTbell and Iso-Seq are trademarks of Pacific Biosciences. BluePippin and SageELF are trademarks of Sage Science, Inc. NGS-go and NGSengine are trademarks of GenDx. All other trademarks are the sole property of their respective owners.