Pre-Processing Workflow Steps
Import Reads
Geneious Prime imports FASTQ files from all major sequencing platforms including Illumina, Oxford Nanopore, and PacBio. Paired-end files are automatically recognized and linked. Batch import handles hundreds of samples at once, and metadata can be attached during import to keep projects organized.
Trim and Filter
The Trim/Filter workflow removes low-quality bases from read ends using quality score thresholds. Adapter sequences are detected and stripped automatically (or you can specify custom adapters). Reads that fall below a minimum length or quality threshold after trimming are discarded to prevent low-quality data from affecting downstream analysis.
Merge Paired-End Reads
For overlapping paired-end reads (such as amplicon sequencing data), Geneious Prime merges the two reads into a single longer read where the overlapping region provides additional quality evidence. Merging produces longer effective read lengths and reduces noise in the overlap region.
De-duplication
PCR duplicates inflate apparent read depth and can skew variant calling. The de-duplication step identifies and removes reads that are exact or near-exact copies of each other, retaining only unique molecules. This step is particularly important in ChIP-seq, amplicon, and low-complexity library preparation protocols.
Error Correction
Sequencing errors introduce false SNPs and indels that complicate assembly and variant calling. Geneious Prime's error correction step uses k-mer frequency analysis to identify and correct likely sequencing errors in reads before assembly or alignment. This step is most impactful for de novo assembly workflows.
Filter Chimeras
Chimeric sequences are artificial hybrids formed during PCR amplification, and they are a significant source of false diversity in amplicon sequencing experiments (16S rRNA, ITS). Geneious Prime filters chimeras using reference-based and de novo detection approaches, flagging and removing chimeric reads before taxonomic classification.
Why Pre-Processing Matters
Skipping or inadequately performing pre-processing steps directly degrades the quality of your downstream results. Low-quality reads misalign to reference genomes, PCR duplicates inflate variant frequencies, and chimeras create spurious OTUs in microbiome studies. Investing time in pre-processing consistently improves assembly quality, variant calling accuracy, and taxonomic classification fidelity.
Geneious Prime advantage: Unlike command-line tools, Geneious Prime's pre-processing steps are visual and interactive. You can inspect quality plots before and after trimming, view adapter contamination statistics, and make informed decisions about threshold parameters without writing any code.