How could I benefit from this workflow?

If you work with novel genomes, the de novo PacBio long read sequencing workflow could be the perfect solution for your sequence assembly needs.  SeqMan NGen assembles PacBio HiFi reads into large and accurate contigs and creates genomic scaffolds, often representing the entire chromosome.

Even with the best data for de novo genome assembly, however, some genomic regions can be difficult to assemble or some long homopolymeric regions may not be completely resolved.  That’s why Lasergene provides additional finishing and editing tools that allow you to improve scaffolds in your draft genomes and create a high-quality finished genome.

What are PacBio HiFi reads, and where do they come from?

PacBio HiFi reads are produced via PacBio’s Sequel HiFi sequencing platform using a hybrid short and long read sequencer mode called “circular consensus sequencing” (CSS). PacBio HiFi reads are shorter but more accurate (see this PacBio post for images) than long-reads produced using other sequencing technologies.

Small sequencing facilities do not usually have access to the PacBio Sequel HiFi sequencing platform or its predecessor, the PacBio RSII sequencer. To obtain reads in PacBio HiFi format, you will likely need to send your samples to a larger facility that supports this new technology.

What are the steps for de novo assembly in Lasergene?

The steps for SeqMan NGen’s basic de novo long-read workflow are:

Step 1:

Launch SeqMan NGen. In the Welcome screen’s default tab (De Novo Assembly and Finishing), choose the PacBio/Nanopore workflow De novo assembly. This is the most commonly-used of SeqMan NGen’s four de novo long-read workflows. (To learn about the other workflows and when to choose them, see our blog post How to Assemble Genomes like a Bioinformatics Pro.)

Step 2: