Whole-genome sequencing and variant discovery in C. elegans

By LaDeana W. Hillier, Gabor T. Marth, Aaron R. Quinlan, D. Dooling, Ginger A. Fewell, Derek W. Barnett, Paul M. Fox, J. Glasscock, M. Hickenbotham, Weichun Huang and 10 more. Nature Methods, 2008

454 citations recorded by the source corpus.

Subfields: Aging, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/61333e9ca3e6544431600096a32f7249804a66fc

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Citations in the corpus

Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood (2008, background): “We strongly suspect that it is an artifact because we also observe GC bias on genomic DNA control, and such bias on the Solexa sequencing platform has recently been reported (38, 39).”
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads (2014, methodology): “Next the processed reads were aligned to the C. elegans genome [17] (version 10) using Bowtie2 [18] (version 2.1.0).”
Personalized Copy-Number and Segmental Duplication Maps using Next-Generation Sequencing (2009, unknown): “Most of these approaches, however, assay only the “unique” regions of the genome 21,23,24.”
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes (2009, methodology): “Mosaik [ 30 ] or SHRiMP [31] 13For example in the Illumina platform (short insert library) , the upstream end sequence is expected to map to the + strand, where the downstream end sequence is expected to map to the - strand; see Figure 5”
Evaluation of next generation sequencing platforms for population targeted sequencing studies (2009, result): “Overall, for the short read platforms read depth coverage decreases with increasing AT content, which is consistent with previous studies [17, 18 ] (Supplemental Figure 1 in Additional data file 3). Roche 454 had one no and one low coverage interval (spanning 4 bp and 59 bp, respectively).”
Applications of next generation sequencing in molecular ecology of non-model organisms (2011, methodology): “GigaBayes (Hillier et al., 2008) and VarScan (Koboldt et al.”
ChIP-Seq: advantages and challenges of a maturing technology (2009, methodology): “Next-generation sequencing has already been applied in many areas, including the sequencing of whole genome”
Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift (2012, background): “Whole-genome sequencing to identify a causative SNP has not been established for D. melanogaster mutants (Hillier et al., 2008; Wang et al., 2010).”
RNA-Seq: a revolutionary tool for transcriptomics (2009, unknown): “Alternatively, a paired-end sequencing strategy, in which short sequences are determined from both ends of a DNA fragmen”
VarScan: variant detection in massively parallel sequencing of individual and pooled samples (2009, background): “New platforms have also enabled rapid sequencing and variant discovery for numerous plants (Ossowski et al., 2008), animals (Hillier et al., 2008) and microbes (Holt et al., 2008).”
Chromatin organization marks exon-intron structure (2009, background): “(iv) To address possible sequencing bias resulting from GC conten”
De novo fragment assembly with short mate-paired reads: Does the read length matter? (2009, unknown): “An analysis in [31] showed that the number of reads uniquely mapped to the human genome grows with the increase in reads length but reaches a plateau after the first ≈ 40 nucleotides.”