Assembly Algorithms for Next-Generation Sequencing Data
By Jason Rafe Miller, Sergey Koren, Granger G. Sutton. Genomics, 2010
1,200 citations recorded by the source corpus.
The emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina/Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages have been created or revised specifically for de novo assembly of next-generation sequencing data. This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/d206ac8572f7480e5d1e92620060a39a8c3fd3ce
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In Molecular Biology
- Sergey Koren
- Adam M. Phillippy
- Michael C. Schatz
- Mihai Pop
- Steven L. Salzberg
- Brian Walenz
- Arang Rhie
- Evan E. Eichler
Citations in the corpus
- Benchmarking of Methods for Genomic Taxonomy (2014, methodology): “To measure the qualities of the draft assemblies, the N50 values were calculated (25).”
- Next-generation transcriptome assembly (2011, methodology): “Although these tools have achieved reasonable success in the assembly of genome”
- Integrating Hi-C links with assembly graphs for chromosome-scale assembly (2018, methodology): “Reads 4 originating from the same locus are identified using assembly software, which can use 5 these overlaps to reconstruct the genome sequence [1, 2].”
- Third generation sequencing: technology and its potential impact on evolutionary biodiversity research (2016, methodology): “Instead of using k-mer assemblies, long reads can be assembled with an overlap-layout-consensus approach (Miller et al., 2010).”
- Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies (2015, background): “49,50 A recent comparison of the latest line of assembly tools shows that IDBA-UD can reconstruct longer contigs with higher accuracy.”
- Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage (2015, neutral): “This may be because an increase in coverage leads to the stochastic accumulation of contradictory reads that cannot be easily reconciled, a limitation of the overlap-layout-consensus algorithm used in assembling the long reads (2,33).”
- Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species (2013, background): “For an overview of these different assembly approaches see [13-16].”