In this technical application note we demonstrate how long reads can be used to study hard-to-sequence regions. We will give an overview of the methods and considerations when targeting genomic regions or transcript sequencing and present various results and examples of applications.
This tutorial provides an overview of the Hierarchical Genome Assembly Process (HGAP4) de novo assembly analysis application. HGAP4 generates accurate de novo assemblies using only PacBio data. HGAP4 is suitable for assembling a wide range of genome sizes and complexity. HGAP4 now includes some support for diploid-aware assembly.
This tutorial provides an overview of the Base Modification and Motif analysis application for identifying common bacterial epigenetic modifications and analyzing methyltransferase recognition motifs. SMRT Analysis software supports epigenetic research by measuring the rate of DNA base incorporation during Single Molecule, Real-Time Sequencing.
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.
This tutorial provides an overview of the Circular Consensus Sequence (CCS) analysis application. The CCS algorithm is used in applications that require distinguishing closely related DNA molecules in the same sample. Applications of CCS include profiling microbial communities, resolving viral populations and accurately identifying somatic variations within heterogeneous tumor cells.
This tutorial provides an overview of the Long Amplicon Analysis (LAA) application. The LAA algorithm generates highly accurate, phased and full-length consensus sequences from long amplicons. Applications of LAA include HLA typing, alternative haplotyping, and localized de novo assemblies of targeted genes.
This tutorial provides an overview of the Isoform Sequencing (Iso-Seq) analysis application. The Iso-Seq application provides reads that span entire transcript isoforms, from the 5′ end to the 3′ polyA-tail. Generation of accurate, full-length transcript sequences greatly simplifies analysis by eliminating the need for transcript reconstruction to infer isoforms using error-prone assembly of short RNA-seq reads.