Piercing the dark matter: bioinformatics of long-range sequencing and mapping

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Structural variant calling: the long and the short of it (2019, unknown): “Nevertheless, multiple papers have re-ported a significant improvement in precision and recall for SV calling using long reads compared to short-read mapping approaches [2, 5, 19, 82, 97 – 99].”
SVIM: structural variant identification using mapped long reads (2018, methodology): “Recently, three methods have been developed for calling SVs based on long reads [23].”
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome (2019, methodology): “To detect structural variants, phase haplotypes and assemble genomes, superior results 14–18 could be obtained with technologies such as PacBio SMRT sequencing 19 and Oxford Nanopore sequencing 20 both of which produce long reads ( > 10 kb).”
The Third Revolution in Sequencing Technology. (2018, background): “Excellent recent reviews focusing on long-read bioinformatics tools can be found elsewhere [17,18].”
Detection of mosaic and population-level structural variants with Sniffles2 (2024, unknown): “This is needed as several genes or regions of the genome remain a ‘dark matter’ 20,32 .”