Get yourself up and running with single molecule real-time (SMRT) sequencing
By Philip Lobb, MSc (field bioinformatics support, Pacific Biosciences) and Christoph König, Ph.D. (field applications support, Pacific Biosciences)
Single Molecule Real-Time (SMRT®) Sequencing:
Technology basics, applications and analysis
Wednesday, March 9
10:30 a.m. – 12:00 p.m.
Auditorium 0125
Between Al-Jazri and Al-Kindi (bldgs. 4 and 5)
(Followed by lunch)
SMRT sequencing is a DNA-sequencing technology characterized by long read lengths and high consensus accuracy regardless of the sequence complexity or GC content of the DNA sample. These characteristics can be harnessed to gain information about genomic regions previously inaccessible to other technologies.
The presentation will cover:
- Principles of the technology
- Its benefits for whole genome de novo assemblies
- Direct full-length cDNA isoform characterization
- Long-range haplotype phasing
- Bioinformatics tools and protocols for downstream data analysis
- Characteristics of the Pacbio RSII and the new Sequel sequencing platforms.
Three Detailed Bioinformatics Training Sessions on SMRT sequencing
Part 2
De-Novo Assembly
Wednesday, March 9
2:00 – 3:00 p.m.
Room 5520, Al-Jazri (bldg. 4)
In this session, we will look at experimental design and key concepts involved in De Novo assembly using the HGAP method. We will also discuss a variety of hybrid assembly approaches. We will show how to import and parameterize an HGAP assembly job in SMRT analysis.
Iso-Seq Full-Length Transcriptome Analysis
Thursday, March 10
10:00 – 11:00 p.m.
Room 5220, Al-Kindi (bldg. 5)
In this session, we look at the Iso-Seq algorithm and discuss the key concepts in the detection of full length Isoform detection. We will then show how to set the parameters for your analysis and how to run an Iso-Seq job.
Long Amplicon Analysis and Multiplexing
Thursday, March 10
11:00 a.m. – 12:00 p.m.
Room 5220, Al-Kindi (bldg. 5)
This session is aimed at those interested in multiplexing for full length amplicon sequencing. Here we will discuss the key concepts in the analysis, including algorithmic design and multiplexing strategies for your experiments.