Short-read sequencing, also known as next-generation sequencing (NGS), is a high-throughput sequencing method that enables rapid and cost-effective analysis of DNA or RNA sequences. It involves breaking the DNA or RNA into short fragments and then simultaneously sequencing millions of these fragmen...
The difficulty of short reads assembly is from high error probability of reads alignment and ambiguity within the genome. This report describes the principle of DNA sequencing and some applications of sequence information, discusses two reference assembly softwares, MAQ and BOWTIE.Chen, Gang...
Onso system’s short-read sequencing chemistry A major contributor to the Onso system’s highly accurate reads is the chemistry. Proprietary sequencing by binding (SBB) chemistry uses native nucleotides, scarless incorporation, and optimized conditions for binding and extension. These innovations result...
Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucle...
The present study provides a comprehensive resource of five BMI and DSE reproductive glands. As the dataset contains both long-read and short-read sequencing data, this rich sequencing dataset paves the avenue for quantifying gene or transcript expression, evaluating alternative splicing, delving novel...
sequencing for only certain limited phases of the assembly, Alpaca uses the full capabilities of the data throughout the entire assembly process: 1) contig structure is primarily formed by long reads that are error corrected by short reads, 2) consensus accuracy is maximized by the highly ...
In this paper, we show how the new generation of sequencing technologies, based on high throughput of short reads, can be used to link site variants and reconstruct multiple full strains of the targeted gene, including those of low concentration in the sample. Our algorithm is based on a ...
We provide a statistical online change point method to help detect CNVs in the sequencing RC data in this paper. This method uses the idea of online searching for change point (or breakpoint) with a Markov chain assumption on the breakpoints loci and an iterative computing process via a ...
PenguiN a software to assemble short read sequencing data on a nucleotide level. In a first step it assembles coding sequences using the information from the translated protein sequences. In a second step it links them across non-coding regions. The main purpose of PenguiN is the assembly of...
Added option (--merge_paired) to accommodate cases where users have multiple read sets for the same sample. If this flag is used, SRST2 will assume that all the input reads belong to the same sample, and outputs will be named as[prefix]__combined.xxx, where SRST2 was run using--outpu...