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Fig. 1 | BMC Bioinformatics

Fig. 1

From: Duet: SNP-assisted structural variant calling and phasing using Oxford nanopore sequencing

Fig. 1

Workflow of Duet. A First, ONT long reads are aligned using Minimap2. B, C To obtain the per-read phasing information (green or brown) with its confidence level (luminance of the color), SNPs (indicated in circles) are called using Clair3 and then phased using WhatsHap. Based on the phased SNPs, the haplotypes of the reads are determined by WhatsHap. D The SV marks on each read are detected by cuteSV. E Three signatures from previous steps are integrated as the signature of the supporting reads. F Duet phases SV and filters out false signals based on the features derived from the signatures in step (E). Description of the signatures and features at step (E) and step (F) is presented in Table 1. T1 to T5 are thresholds for each feature

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