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Fig. 2 | Genome Biology

Fig. 2

From: Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies

Fig. 2

SV detection comparison across different NGS technologies and Software Tools in HCC1395 cancer cell Line. a Violin plot shows the SV detection size ranges for all of SVs called by each NGS platform. The y-axis denotes the SV size in bp, the x-axis denotes the SV types detected by each platform. b Comparison of SVs called by different NGS platform among 10X Chromium linked reads, Illumina short reads, Hi-C, Nanopore, and PacBio call sets. The blue horizontal bars on the left side show the total number of SVs in the specific sequencing platform, black dots on the pink bars denote total SVs called in each sequencing platform. The top black vertical bars display the total concordance calls among the different sequencing platforms. c The heatmap denotes the SV frequencies detected by each tool and technology were generated based on SV location on genome, SV type, and SV frequency which was calculated based on the section “Calculating SV calling frequency and select high-confidence call set”. The platforms include 10X Genomics, Dovetail Hi-C, Illumina, Nanopore, and PacBio. Software tools in the plots include Dell, GrocSVs, Hi-C (Selva), Long Ranger, Manta, Nanosv, NovoBreak, PBSV, Sniffles Nanopore, Sniffles PacBio, and TNscope. The heatmap color denotes the SV frequencies detected by each tool and technology, the dendrograms along the side of the heatmap show similarity and variability how the SVs are clustered. d-e Cross-platform detection of a deletion between 52 and 60Mb region of the chromosome 13. The deletion event was identified by all the replicates and software tools. d Hi-C detection of the deletion event. The outer blackline (outside of the contact matrix) suggests the average read coverage across the entire genome. Red line is raw reads coverage per position. Top left and bottom right part of the contact matrix showing the common contact with 2158 total spanning reads. e Deletion from PacBio data using Ribbon software. The data mapped by minimap2 caller and SV event called by PBSV and Sniffles. The deletion is shown in the middle. The dots in the plot suggest the indeletion events. There are a total 29 reads showing deletion from the PacBio data. f 10X Genomics detected deletion event: Image is generated using loupe browser. The image is showing the barcode interaction between the two coordinates of the chr13 location suggesting deletion. The slope suggests the total number of shared barcodes between two locations. The data was mapped using lariat (Long Ranger) and events called by Long Ranger (SV) and Groc_SVs. g The visualization is generated using SVVIZ from Illumina data. Reads aligning better to the alternate allele than the reference allele will be shown in the set of tracks. Line indicates the break point across 79 reads. The data was mapped using BWA, and SV events were called by Delly, Manta, Novobreak, and TNScope

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