Plotting ONT, PacBio, and 10X Data
This page documents how images are different when created from non-Illumina sequencing data, specifically long reads from Pacific Biosciences or Oxford Nanopore Technology, and linked reads1 from the 10X Genomics platform.
The following images have these sequencing types (in order):
- Illumina
- PacBio (phased)
- ONT (phased)
- 10X
Deletion 1:24804397-24807302
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Illumina shows marked drop in coverage at variant bar, with a large number of discordant pairs supporting variant. In PacBio, ONT, and 10X HP:2 (haplotype 2) shows no evidence for variant, but HP:1 shows drop in coverage and split reads. The last HP is undefined, with reads that could not be phased. Orange reads are long reads, dotted lines indicate split. Green reads are linked, may contain splits (connected with dotted line) or discordant pairs (solid line).
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Illumina shows marked increase in coverage at variant bar, with a large number of discordant pairs supporting variant. In PacBio, ONT, and 10X all three HP tracks include increases in coverage with split read and/or PE evidence. Long-reads that support a duplication call are shown in red and arc back as many times as the read includes the duplicated region.
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Illumina shows marked increase in coverage at variant bar, with a large number of discordant pairs supporting variant. In PacBio, ONT, and 10X HP:1 shows no evidence for variant, but HP:2 shows increase in coverage and split reads.
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Illumina shows very little change in coverage at variant bar, although there is a drop in coverage at both breakpoints. A large number of discordant pairs support the variant. In PacBio and ONT tracks, there is a drop in coverage for both phased haplotypes with most coverage assigned to the undefined haplotype, suggesting that the long reads with inversions do not phase well. Split reads and discordant pairs supporting the inversions are plotted in blue for all sequencing types.
1 As of June 2020, the 10X Genomics linked read sequencing product line was discontinued, therefore samplot will not provide ongoing direct support for linked reads. However, as this functionality is already present, samplot will continue to accept and plot linked reads for the present. More information at https://www.10xgenomics.com/products/linked-reads.