It is now easier and more affordable than ever to do a genome project with PacBio Single Molecule, Real-Time (SMRT) Sequencing—the gold standard for generating contiguous, highly accurate reference genomes. Assembly is no longer a challenge with the wealth of bioinformatics tools developed and optimized for SMRT Sequencing data, enabling you to generate high-quality genome assemblies on any budget.
The PacBio Platform includes an extensive software portfolio that employs key advantages of SMRT (Single Molecule, Real-Time) Sequencing technology: extraordinarily long reads, highest consensus accuracy, uniform coverage and simultaneous epigenetic characterization. Core elements of our analytical portfolio include SMRT Analysis software, DevNet and SMRT Compatible products.
In this article, we review the development of a wide variety of bioinformatics software implementing state-of-the-art algorithms since the introduction of SMRT sequencing technology into the field. We focus on the three major categories of development: read mapping (aligning to reference genomes), de novo assembly, and detection of structural variants. The long SMRT reads benefit all the applications, but they are achievable only through considering the nature of the long reads technology properly.
This tutorial provides a high-level overview of the features contained within the SMRT Link software. SMRT Link is the web-based end-to-end software workflow manager for run design and set-up on the Sequel System, Data Management, and SMRT Analysis.
PacBio CSO Jonas Korlach kicks off the PAG 2017 SMRT Sequencing workshop with acknowledgement of the remarkable work scientists have done with long-read sequencing technology, culminating in more than 2,000 papers so far. Also: Sequel System data, new chemistry and software release, longer libraries, and more.
In this video Roberto Lleras shares new module-based features included in SMRT Link v5.0. He summarizes updates to data management, new applications for minor variant analysis and structural variant analysis and new tools for sending analysis files to PacBio tech support.
PacBio SMRT Sequencing is fast changing the genomics space with its long reads and high consensus sequence accuracy, providing the most comprehensive view of the genome and transcriptome. In this webinar, I will talk about the various data analysis tools available in PacBio’s data analysis suite – SMRT Link – as well as 3rd party tools available. Key applications addressed in this talk are: Genome Assemblies, Structural Variant Analysis, Long Amplicon and Targeted Sequencing, Barcoding Strategies, Iso-Seq Analysis for Full-length Transcript Sequencing
Tremendous flexibility is maintained in the human proteome via alternative splicing, and cancer genomes often subvert this flexibility to promote survival. Identification and annotation of cancer-specific mRNA isoforms is critical to understanding how mutations in the genome affect the biology of cancer cells. While microarrays and other NGS-based methods have become useful for studying transcriptomes, these technologies yield short, fragmented transcripts that remain a challenge for accurate, complete reconstruction of splice variants. The Iso-Seq method developed at PacBio offers the only solution for direct sequencing of full-length, single-molecule cDNA sequences needed to discover biomarkers for early detection and cancer stratification,…
This webinar, presented by Nisha Pillai, provides an overview of bioinformatics approaches for PacBio Single Molecule, Real-Time (SMRT) Sequencing data and discusses the whole genome sequencing application including: assembly workflow designs, an overview analysis tools for de novo assembly of SMRT Sequencing data (HGAP4, FALCON & FALCON-Unzip), and finally best practices and case studies.
2015 SMRT Informatics Developers Conference Presentation Slides: Jason Chin of PacBio highlighted some of the challenges for shotgun assembly while suggesting some potential solutions to obtain diploid assemblies, including the FALCON method.
2015 SMRT Informatics Developers Conference Presentation Slides: Adam English, from the Human Genome Sequencing Center at Baylor College of Medicine presents on the structural variation tools being developed at Baylor.
2015 SMRT Informatics Developers Conference Presentation Slides: Ali Bashir of Mount Sinai School of Medicine discussed methods for characterizing structural variation in human genomes across a variety of coverage levels.
2015 SMRT Informatics Developers Conference Presentation Slides: Gene Myers, Ph.D., Founding Director, Systems Biology Center, Max Planck Institute delivered the keynote presentation. He talked about building efficient assemblers, the importance of random error distribution in sequencing data, and resolving tricky repeats with very long reads. He also encouraged developers to release assembly modules openly, and noted that data should be straightforward to parse since sharing data interfaces is easier than sharing software interfaces.
2015 SMRT Informatics Developers Conference Presentation Slides: Sergey Koren of National Biodefense Analysis and Countermeasures Center (NBACC) provided an overview of the MHAP algorithm, a method for assembling large genomes with Sing-Molecule Sequencing and locality sensitive hashing. Using MHAP, Koren produced a human assembly (CHM1) with a contig N50 of >23 Mb.