NGSNGS: next-generation simulator for next-generation sequencing data.

Summary: With the rapid expansion of the capabilities of the DNA sequencers throughout the different sequencing generations, the quantity of generated data has likewise increased. This evolution has also led to new bioinformatical methods, for which in silico data have become crucial when verifying the accuracy of a model or the robustness of a genomic analysis pipeline. Here, we present a multithreaded next-generation simulator for next-generation sequencing data (NGSNGS), which simulates reads faster than currently available methods and programs.

Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs.

Background: Extrachromosomal circular deoxyribonucleic acid (eccDNA) is evolving as a valuable biomarker, while little is known about its presence in urine.

Methods: Here, we report the discovery and analysis of urinary cell-free eccDNAs (ucf-eccDNAs) in healthy controls and patients with advanced chronic kidney disease (CKD) by Circle-Seq.

Results: Millions of unique ucf-eccDNAs were identified and comprehensively characterised.

Circular DNA in the human germline and its association with recombination.

Extrachromosomal circular DNA (eccDNA) is common in somatic tissue, but its existence and effects in the human germline are unexplored. We used microscopy, long-read DNA sequencing, and new analytic methods to document thousands of eccDNAs from human sperm. EccDNAs derived from all genomic regions and mostly contained a single DNA fragment, although some consisted of multiple fragments.