De Novo Assembly in Geneious Prime

This de novo assembly series shows how to assemble paired-end NGS reads in Geneious Prime without a reference genome. Topics include configuring sensitivity and assembler parameters, normalizing reads with Illumina or Ion Torrent data to cut compute time, and circularizing contigs for accurate mitochondrial and bacterial genome assembly. The series spans three videos, 1 to 4 minutes each.

How to Normalize Your Data

How to do De Novo Assembly of NGS Reads

Configure a de novo assembly of trimmed, paired NGS reads in Geneious Prime, adjusting sensitivity and advanced parameters as needed. Assess the result using the assembly report, coverage statistics, and the insert size histogram.

LENGTH 4 minutes

How to Normalize Your Data

Normalize short, low-error reads, such as Illumina or Ion Torrent data, before de novo assembly using Error Correct and Normalize Reads. Avoid it for long-read platforms, RNA-Seq, ChIP-Seq, or variant discovery, where it can introduce bias.

LENGTH 3 Minutes

How to do Circular Contig Assembly

Create circular contigs for mitochondrial, chloroplast, or bacterial genomes by enabling Circularize Contigs in the de novo assembler's advanced options. Check the Topology column to confirm whether the result is linear or circular.

LENGTH 1 minute