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 ...
Several methods exist to detect insertions from next-generation sequencing short read data, but they generally have low sensitivity. Our contribution is two-fold. First, we introduce INSurVeyor, a fast, sensitive and precise method that detects insertions from next-generation sequencing paired-end ...
For many projects, mixing short and long read data together can have its advantages. Researchers can leverage the lower cost per base, high depth and higher quality data of short read sequencing to generate high confidence SNP and mutation calls, then on top of that data, layer information fro...
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, ...
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...
EMA: An aligner for barcoded short-read sequencing data EMA uses a latent variable model to align barcoded short-reads (such as those produced by 10x Genomics' sequencing platform). More information is available in our paper. The full experimental setup is available here. Install With brew ...
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...
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...
Next-generation sequencing (NGS) is an emerging technology for deciphering genetic variants. Alignment of raw reads to a reference genome is one of the key steps in NGS data analysis. Many algorithms have been developed for alignment of short read sequences since 2008. Users have to make 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...