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PBCE Resources

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

Introduction/Basics

An explanation of Single-Molecule Real-Time Sequencing.
A single-sheet infographic describing how SMRT Sequencing works.
A one page primer and lexicon for PacBio SMRT sequencing.
A description of the PacBio Sequel II system and its capabilities.
A pdf describing RNA-seq on the PacBio using the Kinnex kits.

Grant Support and Funding

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 UMass Chan PBCE facility.

Protocols

A collection of HMW DNA extraction protocols for different organisms
A Technical Note about DNA extraction from Pacific Biosciences
MAS-Seq/Kinnex single-cell RNA sequencing description
MAS-Seq/Kinnex Application Note from PacBio (2023)
MAS-Seq/Kinnex Best Practices from PacBio (2024)
AMPure PB bead creation protocol to DIY AMPure PB beads from AMPure XP for library washes.

Tools

Guidelines from PacBio for Shipping and Handling DNA
Application Options and Sequencing Recommendations for library types, coverage, and insert size

Data and Bioinformatics

Working with BAM Files

NIH Genome WorkBench main site
https://www.ncbi.nlm.nih.gov/tools/gbench/
Working with BAM files (good tutorial)
https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial6/
The Broad’s IGV Site
https://software.broadinstitute.org/software/igv/
Working with BAM files (at IGV)
https://software.broadinstitute.org/software/igv/BAM
BAM format specification for PacBio

PacBio Data Analyses

IsoSeq Tutorial
The User Guide for PacBio's SMRT Link software, which is available on the High Performance Cluster if you wish to run your own 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

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

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Nat Methods. 2024 Jul;21(7):1349-1363
https://pubmed.ncbi.nlm.nih.gov/38849569/

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/

Single-Molecule Poly(A) Tail Sequencing (SM-PATseq) Using the PacBio Platform
Methods Mol Biol. 2024:2723:285-301
https://pubmed.ncbi.nlm.nih.gov/37824077/

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/

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