Bioinformatics challenges of new sequencing technology.

By Mihai Pop, Steven L. Salzberg. Trends in Genetics, 2008

516 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/ed3617a2b4f46ace154bbdaf08d4618381b57a45

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Citations in the corpus

Genome assembly reborn: recent computational challenges (2009, background): “New challenges are posed by recent advances in genome sequencing technologies [12, 13], both due to the sheer size of the data that need to be processed (a single sequencing instrument can provide throughput similar to what was previously only achievable at a genome center), and due to the character”
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery (2010, background): “bacterial artificial chromosomes) is possible with sufficient coverage (Pop and Salzberg 2007).”
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes (2009, background): “…the sequencing of more than 1000 individuals (http://www.1000genomes.org), computational methods for analyzing and managing the massive numbers of the short-read pairs produced by these platforms are urgently needed to effectively detect SNPs, SVs, and copy-number variants (Pop and Salzberg 2008).”
Next-generation sequencing: from basic research to diagnostics. (2009, background): “NGS experiments generate unprecedented volumes of data, which present challenges and opportunities for data management, storage, and, most importantly, analysis ( 61 ).”
Culture-independent molecular techniques for soil microbial ecology (2010, methodology): “of sequence data (Pop and Salzberg, 2008).”
Sequencing technologies — the next generation (2010, background): “The voluminous data produced by these NGS platforms place substantial demands on information technology in terms of data storage, tracking and quality control (see Ref”
The impact of next-generation sequencing on genomics (2011, background): “The full benefit of NGS will not be achieved until bioinformatics are able to maximally interpret and utilize these short-read sequences, including alignment, assembly, etc (Pop and Salzberg, 2008).”
Assembly Algorithms for Next-Generation Sequencing Data (2010, unknown): “These have been reviewed well elsewhere [3,30].”
High‐throughput DNA sequencing – concepts and limitations (2010, unknown): “analysis, time, and personnel [74–77].”
Development of genome-wide SNP assays for rice (2010, background): “7 million SNPs were identified by Shen et al. (2004) and a set of 384,431 high quality SNPs were identified by Feltus et al.”
Repetitive DNA and next-generation sequencing: computational challenges and solutions (2011, background): “In addition to creating gaps, repeats can be erroneously collapsed on top of one another and can cause com‑ plex, misassembled rearrangements 50,51 .”
Applications of next-generation sequencing to the study of biological invasions (2015, background): “However, NGS, with a few exceptions, produces shorter reads than Sanger sequencing, which leads to complications with respect to assembling these short reads into loci, genes, and whole genomes (Pop and Salzberg, 2008).”