This chapter presents new algorithmic methods for next-generation sequencing data. It focuses on the application of resequencing. Here, the authors present the basic definitions and notations that are used throughout the chapter. They also present REad ALigner (REAL), an efficient, sensitive, and ...
Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today’s diverse array of alignm
Prosperi MCF, Prosperi Luciano and Bruselles A, Abbate I, Rozera G, Vincenti D, Solmone MC, Capobianchi MR and Ulivi G, 2011, Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing , BMC bioinformatics , 12 ( 1 ), 5 doi: 10.1186/1471-2105-...
Next-generation sequencing (NGS) offers a unique opportunity for high-throughput genomics and has potential to replace Sanger sequencing in many fields, including de-novo sequencing, re-sequencing, meta-genomics, and characterisation of infectious pathogens, such as viral quasispecies. Although methodologi...
A pipeline that uses read-level features and extra trees/random forest algorithms for accurate and fast detection of somatic mutations in next generation sequencing data - anderdnavarro/RFcaller
Single-cell proteomics enabled by next-generation sequencing or mass spectrometry. Nat. Methods 20, 363–374 (2023). Article CAS PubMed Google Scholar Gatto, L. et al. Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nat. Methods 20, 375–...
GAA is designed to take advantages of different assembly algorithms or sequencing platforms to improve the quality of next-generation sequence (NGS) assemblies. - ghyao/GAA
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As long-read sequencing technologies are becoming increasingly popular, a number of methods have been developed for the discovery and analysis of structural variants (SVs) from long reads. Long reads enable detection of SVs that could not be previously d
References 1 DePristo MAea: A framework for variation discovery and genotyping using next- generation DNA sequencing data. 2011; 43: 491-498. 2 Purcell S, Neale B, Todd-Brown K et al: PLINK: a tool set for whole-genome association and population-based linkage analyses. The Amer...