TL;DR
Highly accurate sequencing approaches have substantially improved the detection of low-frequency variants by reducing technical artifacts and enhancing signal-to-noise ratios.
This work compared the performance of long-read sequencing against short-read sequencing and microarrays, identified two novel non-synonymous variants, including a unique InDel detected exclusively by long-read sequencing, and demonstrated superior detection power, particularly for InDels.
The results indicate that pangenome-based workflows aid improved detection of large variants from targeted sequencing data in the clinical context and suggest that they may contribute to more unified variant detection frameworks for all-size genetic variants in the future.
It is demonstrated that it is possible to sequence permanganate-modified DNA directly using ONT, with minimal effects on the read length, yield, and alignment accuracy, and at high ONT sequencing depth, this approach can identify B-folded vs. single-stranded DNA regions in cells, with ssDNA frequently present across se...
TruPath Genome achieves high-resolution detection of SNVs and indels alongside long-range phasing for CNVs and structural variant (SV) refinement and facilitates telomere-to-telomere assemblies and pangenome development, advancing the understanding of genome biology at an unprecedented scale.
This review compares SNP detection programs such as GATK, BCFtools, FreeBayes, SAMtools, SAMtools, and DeepVariant and their algorithmic structures, namely pileup- based, haplotype-based, and machine-learning approaches and suggests that no single tool is the best.
BLink-seq is presented, a novel Haplotagging method that is compatible with standard short-read next-generation sequencing platforms, is locally reproducible with low-cost reagents, and is scalable for high-throughput sample processing.
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