DNAscope LongRead Nanopore Pipeline

  • Optimized pipeline for SNP/Indel/SV detection;
  • Higher accuracy than Clair3 and Sniffles2;
  • DNAscope for ONT is 3-5x faster;

Access to current DNAscope ONT Performance Datasheet (PDF version)

Fast and Accurate SNP/Indel Calling Pipeline

  • Integrated pipeline from fastq to VCF, perform alignment and variant calling;
  • Output GVCF and VCF files; Supports Chemistry R10.4 and above;
  • Compared to Clair3, Sentieon pipeline reduces SNP and Indel error by over 50%;
  • Preprint published on BioRxiv;

Schematic Diagram of DNAscope LongRead Pipeline: Part of the Genome was assembled into haplotypes to generate more accurate Indel and SV variants.

More than 50% SNP error reduction compared to Clair3.

Total errors fall between roughly 300k and 700k for the HG001–HG007 samples, with Indel making up most errors. Notably, sample HG003 was held out during model training, so its performance reflects true out-of-sample accuracy. In all comparisons, DNAscope LongRead has significant fewer errors than Clair3 in all error categories in all datasets.

Highly Accurate Structural Variants Calling Pipeline

Haplotype-resolved single base resolution SV caller, higher accuracy than Sniffles2 on CMRG regions.

Rapid Alignment and Variant Calling

  • Complete CRAM-VCF analysis within as fast as 13min.
  • Peak Memory under 35GB.

How fast and how cheap? Efficiency metrics for DNAscope LongRead on ONT WGS data (from CRAM to VCF).
Click here – search publications applying DNAscope on Nanopore datasets

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