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PBCE Resources

Resources such as tutorials and tips for working with PacBio data will be posted here.

Introduction/BasicsSequel instrument
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Grant Support and Funding
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  • The UMass Chan PacBio Core Enterprise (PBCE) will provide a formal letter of support to include in grant applications.
  • Pacific Biosciences offers several SMRT Grant Programs to support research that can be applied at the UMMS PBCE facility.

Protocols
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Tools
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Data and Bioinformatics
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Working with BAM Files

PacBio Data Analyses

PacBio Data Information

  • Sequel II and IIe Data Files
  • Coming soon: explanations of the data files you will receive, where to find specific information, what we need from you to carry out analyses (such as genome files for mapping).

Publications
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The PacBio Core Enterprise would be pleased to have you mention us in the acknowledgements section of any publications or presentations of data generated with our support. Our Research Resource Identifier is RRID:SCR_017702.
If you would like to have your publication listed on the Core's website to help highlight the work UMass researchers are doing, email us the reference at PacBio@umassmed.edu.

A collection of papers highlighting applications possible with PacBio technology
https://www.mdpi.com/journal/genes/special_issues/SMRT_sequencing#info

Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads
Ann Hum Genet. 2020 Mar;84(2):125-140
https://www.ncbi.nlm.nih.gov/pubmed/31711268/

Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity
ISME J. 2022 Aug;16(8):1921-1931
https://pubmed.ncbi.nlm.nih.gov/35459792/

Precise therapeutic gene correction by a simple nuclease-induced double-stranded break
Nature. 2019 Apr;568(7753):561-565
https://pubmed.ncbi.nlm.nih.gov/30944467/

RADAR-seq: A RAre DAmage and Repair sequencing method for detecting DNA damage on a genome-wide scale
DNA Repair (Amst). 2019 Aug;80:36-44
https://www.ncbi.nlm.nih.gov/pubmed/31247470/

Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues
J Neurovirol. 2018 Aug;24(4):439-453
https://pubmed.ncbi.nlm.nih.gov/29687407/

The Origin of the Haitian Cholera Outbreak Strain
N Engl J Med. 2011; 364:33-42
https://pubmed.ncbi.nlm.nih.gov/21142692/

Direct Detection and Sequencing of Damaged DNA Bases
Genome Integr. 2011 Dec 20;2:10
https://pubmed.ncbi.nlm.nih.gov/22185597/

Direct Detection of DNA Methylation During Single-Molecule, Real-Time Sequencing
Nat Methods. 2010 Jun;7(6):461-5
https://pubmed.ncbi.nlm.nih.gov/20453866/

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
Nucleic Acids Res. 2012 Feb;40(4):e29
https://pubmed.ncbi.nlm.nih.gov/22156058/

Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia
Nature. 2012 Apr 15;485(7397):260-3
http://www.ncbi.nlm.nih.gov/pubmed/22504184/

Going beyond five bases in DNA Sequencing
Curr Opin Struct Biol. 2012 Jun;22(3):251-61
http://www.ncbi.nlm.nih.gov/pubmed/22575758

Massively multiplex single-molecule oligonucleosome footprinting
Elife. 2020 Dec 2;9:e59404
https://pubmed.ncbi.nlm.nih.gov/33263279/

Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study
Nat Biotechnol. 2021 Sep;39(9):1129-1140
https://pubmed.ncbi.nlm.nih.gov/34504351/

Human and Insect Cell-Produced Recombinant Adeno-Associated Viruses Show Differences in Genome Heterogeneity
Hum Gene Ther. 2022 Apr;33(7-8):371-388
https://pubmed.ncbi.nlm.nih.gov/35293222/

UMMS Deep Sequencing Core logo linking to website

UMMS Molecular Biology Core Labs logo linking to website