You can find additional information on our training where you can search for and download online webinars, e-modules, and other training documents. You can also find various applications (WGS, targeted, epigenetics, RNA and metagenomics) on our sequencing methods page. If you have any questions about our training materials, contact us.
- For genomic or metagenomic DNA, see page 1 of the following: Procedure & checklist – Preparing whole genome and metagenome libraries using SMRTbell prep kit 3.0
- For 16S, see page 7 of the following: Procedure & checklist – Preparing Kinnex libraries from 16S rRNA amplicons
- For other amplicons, see page 3 of the following: Procedure & checklist – Preparing multiplexed amplicon libraries using SMRTbell prep kit 3.0
- For bulk mRNA, see page 1 of the following: Procedure & checklist – Preparing Kinnex libraries using the Kinnex full-length RNA kit
- For single-cell cDNA, see page 1 of the following: Procedure & checklist – Preparing Kinnex libraries using Kinnex single-cell RNA kit
Analysis pipelines are enabled for many applications using SMRT Link.
An overview of HiFi applications and associated analysis tools is also available.
PacBio software is provided for free from our software + bioinformatics webpage, Bioconda, DockerHub, Quay.io, and the PacBio Github. Depending on the type of analysis you need to do, it may be easier to install our SMRT Link software suite or install particular computational tools or workflows to your Linux server or Cloud instance. Please reach out to technical support or Field Applications Bioinformatics Scientists for more information.
HiFi reads are produced using circular consensus sequencing (CCS) mode on PacBio long-read systems. HiFi reads provide base-level resolution with 99.9% single-molecule read accuracy.
HiFi reads can be used across a wide range of SMRT sequencing applications, from whole genome sequencing for de novo assembly, comprehensive variant detection, epigenetic characterization, RNA sequencing and more.
With reads tens of kilobases in length you can readily assemble complete genomes and sequence full-length transcripts. HiFi sequencing provides exceptional read lengths without compromising throughput or accuracy. For more information visit the How does HiFi sequencing work? or HiFi sequencing technology page.
If the wrong barcodes were selected, use one of the two options:
- SMRT Link: use the Data Utility “Undo Demultiplexing” (make sure to run on the parent dataset) and then redo demultiplexing with the correct barcode file using the Data Utility “Demultiplex Barcodes”
- Command line: use lima-undo to undo demultiplexing followed by lima for demultiplexing with the correct barcode fasta file
If barcodes are missing or scores look low and you want to investigate what barcodes might be in the sample that were missed, try using the command line tool lima with –peek-guess
PacBio HiFi reads can detect single-nucleotide variants (SNVs), small indels (<20 bp in length) and structural variants (SVs), such as insertions, deletions, duplications, inversions, translocations, short tandem repeats (STRs), and copy number variants (CNVs). For more details, please see our Variant detection webpage.