Short-read sequencing is widely used in various applications, such as genome sequencing, transcriptome profiling, metagenomics, and epigenetics research. It has revolutionized the field of genomics by enabling the generation of large amounts of sequence data quickly and at a low cost. However, it ...
Liu, W. Muller-Wittig, Quality-score guided error correction for short-read sequencing data using CUDA, Procedia Computer Science 1 (2010) 1129-1138.Shi H, Schmidt B, Liu W, Müller-Wittig W. Quality-score guided error correction for short-read sequencing data using CUDA. Procedia Computer ...
L. et al. Opportunities and challenges in long-read sequencing data analysis. Genome Biol. 21, 30 (2020). Article PubMed PubMed Central Google Scholar Logsdon, G. A., Vollger, M. R. & Eichler, E. E. Long-read human genome sequencing and its applications. Nat. Rev. Genet. 21, ...
MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool. - GATB/MindTheGap
The alignment of short DNA read sequencing data to a human reference genome sequence has become a standard step in the analysis pipeline for short DNA read sequence data. As the rate at which short read DNA sequence data is being produced doubles every 5 months, analysis of this data in a...
However, converting short-read sequencing data into reliable genotype data remains a nontrivial task, especially as RAD-seq is used in systems that have very diverse genomic properties. Here, we present a protocol to analyze RAD-seq data using the Stacks pipeline. This protocol will be of use...
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...
Raw data were visualized via empirical cumulative distribution functions (ECDFs), which display as a step function the distribution, from smallest to largest, of the amount of STR repeat motif found in each read. This allows comparison of the distributions, regardless of sequencing depth. Reads ge...
However, existing algorithms for determining tumor purity, ploidy and copy number are not designed for unmatched short read sequencing data. We describe a methodology and corresponding open source software for estimating tumor purity, copy number, loss of heterozygosity (LOH), and contamination, and ...
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...