Long-Read Genome Assembly & SV Detection Services That Prevent Major Errors

Collapsed gene families, misjoined chromosomes, and missing repeat regions quietly ruin genome assemblies - even when metrics look flawless. Structural variant pipelines miss true breakpoints and flood results with false positives. These failures don’t appear in N50, BUSCO, or summary tables—but they derail interpretation, waste validation efforts, and destroy months of downstream work in HiFi and Nanopore assembly projects.

At AccuraScience, we’ve helped researchers across diverse species and platforms - from PacBio HiFi to Oxford Nanopore - detect and correct subtle yet damaging issues in long-read genome assembly and structural variant (SV) analysis. If your project feels “almost right” but the biology doesn’t line up - or if reviewers are pushing back - we can help.

Our experts specialize in both PacBio structural variant calling and Nanopore SV detection - ensuring accurate breakpoint resolution and minimized false positives.

Eight Pitfalls in Long-Read Genome Assembly and Structural Variant Calling

We’ve reviewed and rescued many long-read genome projects that looked perfect on paper - until closer inspection exposed serious flaws. Here are eight high-impact mistakes we routinely detect and resolve:

1. Overrated N50: Assemblies That Don’t Actually Work

High N50 scores can be misleading. Assemblies that appear successful often contain gene-breaking misjoins or duplicated regions - especially in complex genomes. We validate assemblies using gene models, reference alignment, and coverage profiling.

2. SV Calling: Thousands of Variants, Zero Confidence

SV callsets often include thousands of entries - but many are false positives caused by alignment errors, tool defaults, or lack of orthogonal checks. We apply multiple tools, verify key breakpoints, and filter using sample-specific data.

3. Assembler Selection Without Understanding the Tradeoffs

Choosing an assembler based on popularity - rather than suitability for platform or genome type - leads to critical errors. We test multiple options, simulate edge cases, and validate against trusted loci before committing.

4. Polishing Gone Wrong: "Improvements" That Break Genes

Excessive or poorly configured polishing can introduce frameshifts, soft-clipped junk, or degraded annotations. We polish conservatively, inspect gene model integrity, and compare before-and-after versions to avoid hidden damage.

5. Collapsed Repeats That Silently Delete Biology

Assemblers often collapse tandem repeats or gene families - eliminating biologically critical regions with no obvious warning. We map raw reads to known repeat loci and use coverage peaks and specialized tools to recover what’s missing.

6. Hybrid Assemblies That Mix Strengths - and Weaknesses

Hybrid pipelines (long reads + Hi-C, 10X, or short reads) often introduce new errors if scaffolding or polishing is poorly managed. We validate each stage with orthogonal data, maintain version control, and reject questionable merges.

7. Small Genomes, Big Contamination

Microbial and organellar genomes are prone to hidden contamination. We filter pre- and post-assembly using Kraken2, BMTagger, and database alignments - identifying foreign DNA before it affects downstream conclusions.

8. No Truth Set, No Trust: Validation Gaps in Real Projects

Without simulation or orthogonal validation, teams often over-trust metrics and figures. We use internal truth sets, simulate reads, and validate across platforms to ensure SVs and assemblies hold up under scrutiny.

Read Our Expert Blog on Genome Assembly and SV Detection

We’ve published a deeply detailed blog that explores these pitfalls - with real-world examples and lessons from complex long-read projects using both PacBio and Oxford Nanopore data.

Read the full article:
"Long-Read Assembly and SV Detection: Why So Many Projects Go Wrong - And What Experienced Bioinformaticians Do Differently"

Why Researchers Trust AccuraScience

Founded in 2013, AccuraScience was the first bioinformatics service company in the U.S. offering broad-spectrum customized solutions to academic and industry researchers. Our team of senior bioinformaticians brings over 200 years of combined experience - with deep biological insight and computational rigor. We’ve completed projects for over 180 research institutions across five continents, contributed to NIH-funded grants, and supported peer-reviewed publications and clinical applications.

When It Has to Be Right

Whether you’re trying to resolve a gene family, compare strains, build a reference genome, or trace structural changes across samples - the integrity of your assembly and SV calls determines everything that follows. One error in a contig or breakpoint can derail annotation, confuse downstream analyses, or invalidate core biological conclusions.

We don’t just run pipelines. Our long-read genome analysis services challenge assumptions, validate key findings, and explain what others miss. From HiFi to Nanopore, assembly to SV detection, we help ensure your results are defensible, reproducible, and biologically sound.