PacBio & Nanopore Genome Assembly, Isoform & Direct RNA Analysis, Methylation Profiling & Hybrid Pipelines

Uncertain contigs? Questionable variant calls? Ambiguous isoforms or underpowered hybrid assemblies?

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Many labs struggle to translate long-read data into clean, reviewer-ready results - especially when handling Sequel II HiFi reads, PromethION gigabase runs, or MinION direct RNA.

At AccuraScience, our senior bioinformaticians deliver precise genome assembly services, RNA isoform solutions, robust base modification profiling, and custom hybrid genome integration - for PacBio, Nanopore, and Illumina data alike.

We offer not just services - but deep consulting, flexible support, and tailored solutions that align with your research questions and publication goals.

✅ Who We Support

Whether you generate:

• - Sequel II HiFi reads for high-accuracy assemblies
• - PromethION ultra-long runs for large genomes
• - MinION direct RNA for isoform detection and base modification
• - Or plan to combine Illumina short-reads with long-read data for hybrid polishing

- we help you design, execute, and interpret your project with full transparency, no rigid pipelines, and responsive expert support.

✅ Our Core Expertise

🧬 1) Genome Assembly & Structural Variant Detection

Poor contigs and fragmented references derail downstream analyses and raise reviewer concerns. We build PacBio Sequel II, HiFi, PromethION, and MinION genome assemblies that withstand scrutiny:

• - De novo assemblies using Flye, Canu, HiCanu, Miniasm, tuned for your platform’s error profile and coverage depth.
• - Structural variant detection with Sniffles, Longshot, SVIM, and custom filters for large insertions, deletions, and repeat expansions.
• - Hybrid polishing with Illumina short reads to maximize contiguity while minimizing false positives.

Example: A Sequel II + Illumina hybrid genome project improved N50 by 3X and clarified complex repeat expansions missed by short reads alone.

🧫 2) Iso-Seq & RNA Isoform Analysis

Long-read RNA-seq reveals true isoform structures - but only with robust pipelines and deep experience. We support:

• - Iso-Seq data analysis for Sequel II, HiFi, and legacy SMRT chemistries.
• - Nanopore direct RNA workflows (MinION, PromethION) for basecalling, splicing detection, and kinetic signal analysis.
• - Annotation of novel isoforms and alternative splicing patterns.
• - Pipelines like FLAIR, TALON, FLAMES, IsoQuant with custom QC to catch chimeras and misalignments.

Deliverables: filtered transcript sets, expression tables, isoform plots - all publication-ready.

🧬 3) Base Modification & Methylation Profiling

Going beyond SNP calling, we help you map 5mC, 5hmC, and other kinetic marks using long-read signals:

• - PacBio Sequel II & HiFi methylation analysis using native kinetic data.
• - Nanopore (PromethION, MinION) base modification calling with Megalodon, Remora, Nanopolish, or custom models.
• - Locus-specific methylation frequencies, DMR detection, and integration with SV and isoform results.

Example: We mapped tissue-specific 5mC in PromethION brain reads and correlated it with isoform clusters.

🔁 4) Hybrid Assembly & Cross-Platform Integration

Combining technologies boosts accuracy and cost-effectiveness. Our hybrid pipelines cover:

• - Sequel II + Illumina hybrid genome assembly with Unicycler, MaSuRCA, and custom polishing.
• - PromethION hybrid pipelines for complex, large genomes.
• - QC steps to prevent over-polishing and coverage bias.
• - Hybrid RNA quantification for isoform-level expression resolution.

✅ 📚 Practical Insights from Our Experts

• → Illumina, PacBio, or Oxford Nanopore: Which One To Choose? - a clear comparison of major sequencing platforms and when to choose each.
• → Practical Thoughts on Long-Read Genome Assembly, Isoforms, Methylation, and Hybrid Integration - real-world lessons and recommendations from our projects.

Explore the 10 Reasons Why Researchers Choose Us →

Reason #1: 200 years of combined experience in bioinformatics
Reason #2: Deep understanding of both the biology and the computer
Reason #3: Top-level expertise possessed by our bioinformaticians
Reason #4: Wide range of bioinformatics and data modeling solutions that we cover
Reason #5: Researchers from 180 organizations can’t all be wrong!
Reason #6: We are cost-effective
Reason #7: We guarantee to do it “right”!
Reason #8: We will assist you in paper reviews
Reason #9: We will assist you in grant writing
Reason #10: See how researchers have evaluated us

✅ What You Can Expect

• - Transparent, milestone-based workflows
• - Rigorous QC at every step
• - Direct access to your lead bioinformatician - no layers of managers
• - Well-documented results, ready for publication and peer review