Short read fragment assembly of bacterial genomes.

By Mark J. P. Chaisson, Pavel A. Pevzner. Genome Research, 2008

482 citations recorded by the source corpus.

In the last year, high-throughput sequencing technologies have progressed from proof-of-concept to production quality. While these methods produce high-quality reads, they have yet to produce reads comparable in length to Sanger-based sequencing. Current fragment assembly algorithms have been implemented and optimized for mate-paired Sanger-based reads, and thus do not perform well on short reads produced by short read technologies. We present a new Eulerian assembler that generates nearly optimal short read assemblies of bacterial genomes and describe an approach to assemble reads in the case of the popular hybrid protocol when short and long Sanger-based reads are combined.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/101941da6afb2480153551802249ffe5a72640d1

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Citations in the corpus

Bioinformatics challenges of new sequencing technology. (2008, methodology): “Chaisson and Pevzner [ 27 ] showed their assembler (Euler-SR) is able to generate high-quality assemblies of bacterial genomes from 454 reads and of BAC clones from Solexa reads.”
Sequence-specific error profile of Illumina sequencers (2011, background): “Nevertheless, at present, the only sensible way of filling the gaps of the Illumina sequencer reads appears to be combining the information from other experimental methods, including other NGS platforms that carry mutually complementary information (36,37).”
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing (2012, methodology): “The assemblers are EULER-SR (Chaisson and Pevzner, 2008), IDBA (Peng et al.”
An Integrated Pipeline for de Novo Assembly of Microbial Genomes (2012, methodology): “These include tools for base calling of the images from the sequencer [1,2], error correction of the sequence reads [3,4], removal of adapter sequence contamination [5], contig assembly [6,7], and scaffolding [8–10].”
A Primer on Metagenomics (2010, methodology): “The EULER assembler [49,50] was the first to present this technique using de Bruijn graphs.”
GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes (2018, background): “While many bacterial genomes assemblers used the minimum or the greedy algorithm for detecting multiplicity, which is simply assuming every tandem repeat contig has multiplicity two and constructing the assembly as a path that traverses the repeat twice [44-46].”
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. (2012, background): “Assembly The currently accepted methods most capable of assembling NGS data utilize Kmer DeBruijn graph traversalbased methods, including programs such as Velvet, SOAPdenovo, ALLPATHS, ABySS, the CLC Bio commercial www.sciencedirect.com product as well as number of newer assemblers under development”
BayesHammer: Bayesian clustering for error correction in single-cell sequencing (2012, methodology): “In contrast, EULER-SR [9] and CAMEL [2] correct reads and do not make strong assumptions on coverage (both tools have been used for single-cell assembly projects [2]) which makes these tools suitable for comparison to BAYESHAMMER.”
The MaSuRCA genome assembler (2013, methodology): “Recently developed assemblers that use the de Bruijn strategy include Allpaths-LG (Gnerre et al., 2010), SOAPdenovo (Li et al., 2008), Velvet (Zerbino and Birney, 2008), EULER-SR (Chaisson and Pevzner, 2008) and ABySS (Simpson et al., 2009).”
Aggressive assembly of pyrosequencing reads with mates (2008, methodology): “Newbler was updated to accept non-pyro data (Roche, 2007), and Euler was modified to accept pyro data in a version called Euler-SR (Chaisson and Pevzner, 2008).”
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery (2010, methodology): “A variety of tools that are beyond the scope of this paper have been developed for alignment and de novo assembly of short reads (for examples, see Warren et al. 2007; Dohm et al. 2007; Jeck et al. 2007; De Bona et al. 2008; Chaisson and Pevzner 2008; Li et al. 2008a; Smith et al. 2008; Zerbino and ”
De novo fragment assembly with short mate-paired reads: Does the read length matter? (2009, methodology): “2001) that correct reads based on k-mer multiplicities, EULER-USR corrects reads based on how they map to repeat graphs (Pevzner et al. 2001; Chaisson and Pevzner 2008), a generalization of the de Bruijn graphs.”
ABySS: a parallel assembler for short read sequence data. (2009, methodology): “We have developed a similar process to EULER-SR (Chaisson and Pevzner 2008), Velvet (Zerbino and Birney 2008), and Edena (Hernandez et al.”
Assembly Algorithms for Next-Generation Sequencing Data (2010, unknown): “It was subsequently modified for short 454 GS20 reads [53], even shorter unpaired Illumina/Solexa reads [54], and paired-end Solexa reads [55].”
Next-generation sequencing: from basic research to diagnostics. (2009, background): “Software for de novo assembly includes Edina (70), EULER-SR ( 74 ), SHARCGS (75), SSAKE (69), Velvet (76), and SOAPdenovo (http://soap.genomics.org.cn/).”
Efficient de novo assembly of large genomes using compressed data structures. (2012, methodology): “We then perform the standard assembly graph post-processing step of removing tips from the graph where a vertex only has a connection in one direction (Chaisson and Pevzner 2008; Zerbino and Birney 2008; Simpson et al. 2009; Li et al. 2010b).”
De novo assembly of human genomes with massively parallel short read sequencing. (2010, methodology): “A few short read assemblers, including Velvet (Zerbino and Birney 2008), ALLPATHS (Butler et al. 2008), and EULER-SR (Chaisson and Pevzner 2008), have adopted this algorithm, explicitly or implicitly, and have been implemented and shown very promising performances.”